Methods and Materials for Using Measles Viruses

ABSTRACT

This document provides methods and materials involved in using measles viruses. For example, methods and materials for identifying mammals (e.g., humans) likely to respond to standard measles virus vaccines or standard measles virus-based therapies as well as methods and materials for identifying mammals (e.g., humans) unlikely to respond to standard measles virus vaccines or standard measles virus-based therapies are provided.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a divisional of U.S. application Ser. No.15/907,056, filed Feb. 27, 2018, which claims the benefit of U.S.Provisional Application Ser. No. 62/464,581, filed Feb. 28, 2017. Thedisclosure of the prior applications are considered part of (and areincorporated by reference in) the disclosure of this application.

STATEMENT AS TO FEDERALLY SPONSORED RESEARCH

This invention was made with government support under AI033144 andAI048793 awarded by National Institutes of Health. The government hascertain rights in the invention.

BACKGROUND 1. Technical Field

This document relates to methods and materials involved in using measlesviruses. For example, this document provides methods and materials foridentifying mammals (e.g., humans) likely to respond to standard measlesvirus vaccines or standard measles virus-based therapy (e.g., measlesvirus-based oncolytic therapy or measles virus vectored vaccines). Thisdocument also provides methods and materials for identifying mammals(e.g., humans) unlikely to respond to standard measles virus vaccines orstandard measles virus-based therapy (e.g., measles virus-basedoncolytic therapy or measles virus vectored vaccines).

2. Background Information

Measles remains a disease of public health concern in the developingworld and well-developed countries with multiple outbreaks even amongpopulations with high vaccine coverage. From 2010 to date, the Europeanregion registered 135,600 measles cases, and the US experienced 1,381measles cases in 27 states. Several population-based studies estimatedthat 2 to 10% of vaccine recipients do not develop or sustainmeasles-specific protective immunity after two doses of MMR vaccine(Bednarczyk et al., Am. J. Epid., 184:148-56 (2016); Haralambieva etal., Vaccine, 29:4485-4491 (2011); Haralambieva et al., Ex. Rev.Vaccines, 12:57-70 (2013); Poland and Jacobson, Vaccine, 30:103-104(2012); and Whitaker and Poland, Vaccine, 32:4703-4704 (2014)). Themechanisms behind vaccine failure are unknown.

SUMMARY

This document provides methods and materials involved in using measlesviruses. For example, this document provides methods and materials foridentifying mammals (e.g., humans) likely to respond to standard measlesvirus vaccines or measles virus-based therapies (e.g., oncolytic measlesvirus-based therapies). As described herein, a human identified ashaving the major allele T of CD46 rs2724374, the major allele A of CD46rs2724384, the major allele A of IFI44L rs273259, the major allele T ofIFI44L rs1333973, the major allele C of CD46 rs4844619, the major alleleC of CD46 rs2466572, the major allele T of CD46 rs2724360, the majorallele G of CD46 rs6657476, the major allele A of CD46 rs4844390, themajor allele A of IFI44L rs4650590, the major allele G of IFI44Lrs6693207, the major allele A of IFI44L rs273255, the major allele G ofIFI44L rs273261, the major allele A of IFI44L rs273256, the major alleleA of IFI44L rs273244, the major allele T of LOC101929385 rs11118612, themajor allele C of LOC101929385 rs4844392, the major allele A ofLOC101929385 rs66532523, the major allele G of LOC101929385 rs4844620,the major allele G of intergenic rs2761437, the major allele T ofintergenic rs2796265, the major allele G of intergenic rs2761434, themajor allele T of intergenic rs56075814, the major allele T ofintergenic rs6669384, the major allele T of intergenic rs55935450, themajor allele C of intergenic rs11118668, the major allele T ofintergenic rs1318653, the major allele T of intergenic rs61821293, themajor allele G of intergenic rs273238, the major allele A of intergenicrs12026737, the minor allele C of CD46 rs11806810, or combinationsthereof can be classified as being a human who is more likely tofavorably respond to standard measles virus vaccination protocols and/ormeasles virus-based therapies (e.g., oncolytic measles virus-basedtherapies). In some cases, such identified humans can be administered astandard measles virus vaccination protocol when undergoing measlesvirus vaccination or a measles virus-based therapy (e.g., an oncolyticmeasles virus-based therapy) when being treated for cancer or otherconditions.

This document also provides methods and materials for identifyingmammals (e.g., humans) that are less likely to respond to standardmeasles virus vaccines or measles virus-based therapies (e.g., oncolyticmeasles virus-based therapies). As described herein, a human identifiedas having the minor allele G of CD46 rs2724374, the minor allele G ofCD46 rs2724384, the minor allele G of IFI44L rs273259, the minor alleleA of IFI44L rs1333973, the minor allele T of CD46 rs4844619, the minorallele A of CD46 rs2466572, the minor allele C of CD46 rs2724360, theminor allele T of CD46 rs6657476, the minor allele G of CD46 rs4844390,the minor allele G of IFI44L rs4650590, the minor allele A of IFI44Lrs6693207, the minor allele T of IFI44L rs273255, the minor allele A ofIFI44L rs273261, the minor allele C of IFI44L rs273256, the minor alleleT of IFI44L rs273244, the minor allele A of LOC101929385 rs11118612, theminor allele G of LOC101929385 rs4844392, the minor allele C ofLOC101929385 rs66532523, the minor allele A of LOC101929385 rs4844620,the minor allele A of intergenic rs2761437, the minor allele C ofintergenic rs2796265, the minor allele A of intergenic rs2761434, theminor allele C of intergenic rs56075814, the minor allele C ofintergenic rs6669384, the minor allele A of intergenic rs55935450, theminor allele T of intergenic rs11118668, the minor allele C ofintergenic rs1318653, the minor allele G of intergenic rs61821293, theminor allele A of intergenic rs273238, the minor allele C of intergenicrs12026737, the major allele G of CD46 rs11806810 or combinationsthereof can be classified as being a human who is less likely tofavorably respond to standard measles virus vaccination protocols and/ormeasles virus-based therapies (e.g., oncolytic measles virus-basedtherapies). In some cases, humans identified as having two or more ofthe minor alleles listed in this paragraph (e.g., a homozygous minorallele genotype) can be less likely to favorably respond to standardmeasles virus vaccination protocols and/or measles virus-based therapies(e.g., oncolytic measles virus-based therapies). In some cases, suchidentified humans can be administered an enhanced measles virusvaccination protocol (e.g., different dosage, number of doses, route ofvaccination, and/or modified vaccine formulation) when undergoingmeasles virus vaccination or a modified measles virus-based therapy ortreatment (e.g., non-measles virus-based cancer therapy in the case whenmeasles virus-based oncolytic therapy is considered as a treatmentoption). Examples of such other treatments include, without limitation,other non-measles oncolytic virotherapy agents (e.g., adenovirus, Herpessimplex virus, poliovirus, parvovirus, reovirus, New Castle virus,Coxsackie virus, or vaccinia) as described elsewhere (Russell et al.,Nat. Biotechnol., 30(7):658-70 (2012) and targeted cancer therapy orstandard chemotherapy treatments for specific cancers/malignancies suchas those described elsewhere (Mikhael et al., Mayo Clin. Proc.,88(7):777 (2013); Dispenzieri et al., Blood, 122(26):4172-81 (2013);Aletti et al., Mayo Clin. Proc., 82(6):751-70 (2007); Grunewald et al.,Best Pract Res. Clin. Obstet. Gynaecol., pii: S1521-6934(16)30142-0(2016); Rodriguez-Freixinos et al., Expert Opin. Pharmacother17(8):1063-76 (2016); Hans-Georg Wirsching et al., Handb. Clin. Neurol.,134:381-97 (2016); and Johnson et al., Semin. Oncol., 41(4):511-22(2014)).

In general, one aspect of this document features a method foridentifying a human as being likely to respond to a measles virusvaccination. The method comprises, or consists essentially of, (a)detecting the presence of the major allele T of CD46 rs2724374, themajor allele A of CD46 rs2724384, the major allele A of IFI44L rs273259,the major allele T of IFI44L rs1333973, the major allele C of CD46rs4844619, the major allele C of CD46 rs2466572, the major allele T ofCD46 rs2724360, the major allele G of CD46 rs6657476, the major allele Aof CD46 rs4844390, the major allele A of IFI44L rs4650590, the majorallele G of IFI44L rs6693207, the major allele A of IFI44L rs273255, themajor allele G of IFI44L rs273261, the major allele A of IFI44Lrs273256, the major allele A of IFI44L rs273244, the major allele T ofLOC101929385 rs11118612, the major allele C of LOC101929385 rs4844392,the major allele A of LOC101929385 rs66532523, the major allele G ofLOC101929385 rs4844620, the major allele G of intergenic rs2761437, themajor allele T of intergenic rs2796265, the major allele G of intergenicrs2761434, the major allele T of intergenic rs56075814, the major alleleT of intergenic rs6669384, the major allele T of intergenic rs55935450,the major allele C of intergenic rs11118668, the major allele T ofintergenic rs1318653, the major allele T of intergenic rs61821293, themajor allele G of intergenic rs273238, the major allele A of intergenicrs12026737, or the minor allele C of CD46 rs11806810 in a sampleobtained from the human, and (b) classifying the human as being likelyto respond to the measles virus vaccination. The method can comprisedetecting the presence of the major allele T of CD46 rs2724374, themajor allele A of CD46 rs2724384, the major allele A of IFI44L rs273259,the major allele T of IFI44L rs1333973, the major allele C of CD46rs4844619, the major allele C of CD46 rs2466572, the major allele T ofCD46 rs2724360, the major allele G of CD46 rs6657476, the major allele Aof CD46 rs4844390, the major allele A of IFI44L rs4650590, the majorallele G of IFI44L rs6693207, the major allele A of IFI44L rs273255, themajor allele G of IFI44L rs273261, the major allele A of IFI44Lrs273256, the major allele A of IFI44L rs273244, the major allele T ofLOC101929385 rs11118612, the major allele C of LOC101929385 rs4844392,the major allele A of LOC101929385 rs66532523, the major allele G ofLOC101929385 rs4844620, the major allele G of intergenic rs2761437, themajor allele T of intergenic rs2796265, the major allele G of intergenicrs2761434, the major allele T of intergenic rs56075814, the major alleleT of intergenic rs6669384, the major allele T of intergenic rs55935450,the major allele C of intergenic rs11118668, the major allele T ofintergenic rs1318653, the major allele T of intergenic rs61821293, themajor allele G of intergenic rs273238, the major allele A of intergenicrs12026737, and the minor allele C of CD46 rs11806810 in the sample. Themeasles virus vaccination can be a measles, mumps, and rubella vaccine.

In another aspect, this document features a method for providing a humanwith a measles virus vaccination. The method comprises, or consistsessentially of, (a) detecting the presence of the major allele T of CD46rs2724374, the major allele A of CD46 rs2724384, the major allele A ofIFI44L rs273259, the major allele T of IFI44L rs1333973, the majorallele C of CD46 rs4844619, the major allele C of CD46 rs2466572, themajor allele T of CD46 rs2724360, the major allele G of CD46 rs6657476,the major allele A of CD46 rs4844390, the major allele A of IFI44Lrs4650590, the major allele G of IFI44L rs6693207, the major allele A ofIFI44L rs273255, the major allele G of IFI44L rs273261, the major alleleA of IFI44L rs273256, the major allele A of IFI44L rs273244, the majorallele T of LOC101929385 rs11118612, the major allele C of LOC101929385rs4844392, the major allele A of LOC101929385 rs66532523, the majorallele G of LOC101929385 rs4844620, the major allele G of intergenicrs2761437, the major allele T of intergenic rs2796265, the major alleleG of intergenic rs2761434, the major allele T of intergenic rs56075814,the major allele T of intergenic rs6669384, the major allele T ofintergenic rs55935450, the major allele C of intergenic rs11118668, themajor allele T of intergenic rs1318653, the major allele T of intergenicrs61821293, the major allele G of intergenic rs273238, the major alleleA of intergenic rs12026737, or the minor allele C of CD46 rs11806810 ina sample obtained from the human, and (b) administering a measles virusvaccine to the human. The method can comprise detecting the presence ofthe major allele T of CD46 rs2724374, the major allele A of CD46rs2724384, the major allele A of IFI44L rs273259, the major allele T ofIFI44L rs1333973, the major allele C of CD46 rs4844619, the major alleleC of CD46 rs2466572, the major allele T of CD46 rs2724360, the majorallele G of CD46 rs6657476, the major allele A of CD46 rs4844390, themajor allele A of IFI44L rs4650590, the major allele G of IFI44Lrs6693207, the major allele A of IFI44L rs273255, the major allele G ofIFI44L rs273261, the major allele A of IFI44L rs273256, the major alleleA of IFI44L rs273244, the major allele T of LOC101929385 rs11118612, themajor allele C of LOC101929385 rs4844392, the major allele A ofLOC101929385 rs66532523, the major allele G of LOC101929385 rs4844620,the major allele G of intergenic rs2761437, the major allele T ofintergenic rs2796265, the major allele G of intergenic rs2761434, themajor allele T of intergenic rs56075814, the major allele T ofintergenic rs6669384, the major allele T of intergenic rs55935450, themajor allele C of intergenic rs11118668, the major allele T ofintergenic rs1318653, the major allele T of intergenic rs61821293, themajor allele G of intergenic rs273238, the major allele A of intergenicrs12026737, and the minor allele C of CD46 rs11806810 in the sample. Themeasles virus vaccine is a measles, mumps, and rubella vaccine.

In another aspect, this document features a method for identifying ahuman as being unlikely to respond to a measles virus vaccination. Themethod comprises, or consists essentially of, (a) detecting the presenceof the minor allele G of CD46 rs2724374, the minor allele G of CD46rs2724384, the minor allele G of IFI44L rs273259, the minor allele A ofIFI44L rs1333973, the minor allele T of CD46 rs4844619, the minor alleleA of CD46 rs2466572, the minor allele C of CD46 rs2724360, the minorallele T of CD46 rs6657476, the minor allele G of CD46 rs4844390, theminor allele G of IFI44L rs4650590, the minor allele A of IFI44Lrs6693207, the minor allele T of IFI44L rs273255, the minor allele A ofIFI44L rs273261, the minor allele C of IFI44L rs273256, the minor alleleT of IFI44L rs273244, the minor allele A of LOC101929385 rs11118612, theminor allele G of LOC101929385 rs4844392, the minor allele C ofLOC101929385 rs66532523, the minor allele A of LOC101929385 rs4844620,the minor allele A of intergenic rs2761437, the minor allele C ofintergenic rs2796265, the minor allele A of intergenic rs2761434, theminor allele C of intergenic rs56075814, the minor allele C ofintergenic rs6669384, the minor allele A of intergenic rs55935450, theminor allele T of intergenic rs11118668, the minor allele C ofintergenic rs1318653, the minor allele G of intergenic rs61821293, theminor allele A of intergenic rs273238, the minor allele C of intergenicrs12026737, or the major allele G of CD46 rs11806810 in a sampleobtained from the human, and (b) classifying the human as being unlikelyto respond to the measles virus vaccination. The method can comprisedetecting the presence of the minor allele G of CD46 rs2724374, theminor allele G of CD46 rs2724384, the minor allele G of IFI44L rs273259,the minor allele A of IFI44L rs1333973, the minor allele T of CD46rs4844619, the minor allele A of CD46 rs2466572, the minor allele C ofCD46 rs2724360, the minor allele T of CD46 rs6657476, the minor allele Gof CD46 rs4844390, the minor allele G of IFI44L rs4650590, the minorallele A of IFI44L rs6693207, the minor allele T of IFI44L rs273255, theminor allele A of IFI44L rs273261, the minor allele C of IFI44Lrs273256, the minor allele T of IFI44L rs273244, the minor allele A ofLOC101929385 rs11118612, the minor allele G of LOC101929385 rs4844392,the minor allele C of LOC101929385 rs66532523, the minor allele A ofLOC101929385 rs4844620, the minor allele A of intergenic rs2761437, theminor allele C of intergenic rs2796265, the minor allele A of intergenicrs2761434, the minor allele C of intergenic rs56075814, the minor alleleC of intergenic rs6669384, the minor allele A of intergenic rs55935450,the minor allele T of intergenic rs11118668, the minor allele C ofintergenic rs1318653, the minor allele G of intergenic rs61821293, theminor allele A of intergenic rs273238, the minor allele C of intergenicrs12026737, and the major allele G of CD46 rs11806810 in the sample. Themeasles virus vaccination is a measles, mumps, and rubella vaccine.

In another aspect, this document features a method for providing a humanwith a measles virus vaccination. The method comprises, or consistsessentially of, (a) detecting the presence of the minor allele G of CD46rs2724374, the minor allele G of CD46 rs2724384, the minor allele G ofIFI44L rs273259, the minor allele A of IFI44L rs1333973, the minorallele T of CD46 rs4844619, the minor allele A of CD46 rs2466572, theminor allele C of CD46 rs2724360, the minor allele T of CD46 rs6657476,the minor allele G of CD46 rs4844390, the minor allele G of IFI44Lrs4650590, the minor allele A of IFI44L rs6693207, the minor allele T ofIFI44L rs273255, the minor allele A of IFI44L rs273261, the minor alleleC of IFI44L rs273256, the minor allele T of IFI44L rs273244, the minorallele A of LOC101929385 rs11118612, the minor allele G of LOC101929385rs4844392, the minor allele C of LOC101929385 rs66532523, the minorallele A of LOC101929385 rs4844620, the minor allele A of intergenicrs2761437, the minor allele C of intergenic rs2796265, the minor alleleA of intergenic rs2761434, the minor allele C of intergenic rs56075814,the minor allele C of intergenic rs6669384, the minor allele A ofintergenic rs55935450, the minor allele T of intergenic rs11118668, theminor allele C of intergenic rs1318653, the minor allele G of intergenicrs61821293, the minor allele A of intergenic rs273238, the minor alleleC of intergenic rs12026737, or the major allele G of CD46 rs11806810 ina sample obtained from the human, and (b) administering an enhancedmeasles virus vaccine to the human or administering a measles virusvaccine at least three times to the human. The method can comprisedetecting the presence of the minor allele G of CD46 rs2724374, theminor allele G of CD46 rs2724384, the minor allele G of IFI44L rs273259,the minor allele A of IFI44L rs1333973, the minor allele T of CD46rs4844619, the minor allele A of CD46 rs2466572, the minor allele C ofCD46 rs2724360, the minor allele T of CD46 rs6657476, the minor allele Gof CD46 rs4844390, the minor allele G of IFI44L rs4650590, the minorallele A of IFI44L rs6693207, the minor allele T of IFI44L rs273255, theminor allele A of IFI44L rs273261, the minor allele C of IFI44Lrs273256, the minor allele T of IFI44L rs273244, the minor allele A ofLOC101929385 rs11118612, the minor allele G of LOC101929385 rs4844392,the minor allele C of LOC101929385 rs66532523, the minor allele A ofLOC101929385 rs4844620, the minor allele A of intergenic rs2761437, theminor allele C of intergenic rs2796265, the minor allele A of intergenicrs2761434, the minor allele C of intergenic rs56075814, the minor alleleC of intergenic rs6669384, the minor allele A of intergenic rs55935450,the minor allele T of intergenic rs11118668, the minor allele C ofintergenic rs1318653, the minor allele G of intergenic rs61821293, theminor allele A of intergenic rs273238, the minor allele C of intergenicrs12026737, and the major allele G of CD46 rs11806810 in the sample. Themethod can comprises administering the enhanced measles virus vaccine,and wherein the enhanced measles virus vaccine comprises adjuvantshaving the ability to increase surface expression of CD46 orupregulation of IFI44L. The method can comprises administering themeasles virus vaccine, and the measles virus vaccine can be a measles,mumps, and rubella vaccine.

In another aspect, this document features a method for identifying ahuman having cancer (or other condition requiring measles virus-basedtherapy) as being likely to respond to a measles virus-based therapy.The method comprises, or consists essentially of, (a) detecting thepresence of the major allele T of CD46 rs2724374, the major allele A ofCD46 rs2724384, the major allele A of IFI44L rs273259, the major alleleT of IFI44L rs1333973, the major allele C of CD46 rs4844619, the majorallele C of CD46 rs2466572, the major allele T of CD46 rs2724360, themajor allele G of CD46 rs6657476, the major allele A of CD46 rs4844390,the major allele A of IFI44L rs4650590, the major allele G of IFI44Lrs6693207, the major allele A of IFI44L rs273255, the major allele G ofIFI44L rs273261, the major allele A of IFI44L rs273256, the major alleleA of IFI44L rs273244, the major allele T of LOC101929385 rs11118612, themajor allele C of LOC101929385 rs4844392, the major allele A ofLOC101929385 rs66532523, the major allele G of LOC101929385 rs4844620,the major allele G of intergenic rs2761437, the major allele T ofintergenic rs2796265, the major allele G of intergenic rs2761434, themajor allele T of intergenic rs56075814, the major allele T ofintergenic rs6669384, the major allele T of intergenic rs55935450, themajor allele C of intergenic rs11118668, the major allele T ofintergenic rs1318653, the major allele T of intergenic rs61821293, themajor allele G of intergenic rs273238, the major allele A of intergenicrs12026737, or the minor allele C of CD46 rs11806810 in a sampleobtained from the human, and (b) classifying the human as being likelyto respond to the measles virus-based oncolytic treatment. The methodcan comprise detecting the presence of the major allele T of CD46rs2724374, the major allele A of CD46 rs2724384, the major allele A ofIFI44L rs273259, the major allele T of IFI44L rs1333973, the majorallele C of CD46 rs4844619, the major allele C of CD46 rs2466572, themajor allele T of CD46 rs2724360, the major allele G of CD46 rs6657476,the major allele A of CD46 rs4844390, the major allele A of IFI44Lrs4650590, the major allele G of IFI44L rs6693207, the major allele A ofIFI44L rs273255, the major allele G of IFI44L rs273261, the major alleleA of IFI44L rs273256, the major allele A of IFI44L rs273244, the majorallele T of LOC101929385 rs11118612, the major allele C of LOC101929385rs4844392, the major allele A of LOC101929385 rs66532523, the majorallele G of LOC101929385 rs4844620, the major allele G of intergenicrs2761437, the major allele T of intergenic rs2796265, the major alleleG of intergenic rs2761434, the major allele T of intergenic rs56075814,the major allele T of intergenic rs6669384, the major allele T ofintergenic rs55935450, the major allele C of intergenic rs11118668, themajor allele T of intergenic rs1318653, the major allele T of intergenicrs61821293, the major allele G of intergenic rs273238, the major alleleA of intergenic rs12026737, and the minor allele C of CD46 rs11806810 inthe sample.

In another aspect, this document features a method for treating a humanhaving cancer. The method comprises, or consists essentially of, (a)detecting the presence of the major allele T of CD46 rs2724374, themajor allele A of CD46 rs2724384, the major allele A of IFI44L rs273259,the major allele T of IFI44L rs1333973, the major allele C of CD46rs4844619, the major allele C of CD46 rs2466572, the major allele T ofCD46 rs2724360, the major allele G of CD46 rs6657476, the major allele Aof CD46 rs4844390, the major allele A of IFI44L rs4650590, the majorallele G of IFI44L rs6693207, the major allele A of IFI44L rs273255, themajor allele G of IFI44L rs273261, the major allele A of IFI44Lrs273256, the major allele A of IFI44L rs273244, the major allele T ofLOC101929385 rs11118612, the major allele C of LOC101929385 rs4844392,the major allele A of LOC101929385 rs66532523, the major allele G ofLOC101929385 rs4844620, the major allele G of intergenic rs2761437, themajor allele T of intergenic rs2796265, the major allele G of intergenicrs2761434, the major allele T of intergenic rs56075814, the major alleleT of intergenic rs6669384, the major allele T of intergenic rs55935450,the major allele C of intergenic rs11118668, the major allele T ofintergenic rs1318653, the major allele T of intergenic rs61821293, themajor allele G of intergenic rs273238, the major allele A of intergenicrs12026737, or the minor allele C of CD46 rs11806810 in a sampleobtained from the human, and (b) administering a measles virus-basedoncolytic treatment to the human. The method can comprise detecting thepresence of the major allele T of CD46 rs2724374, the major allele A ofCD46 rs2724384, the major allele A of IFI44L rs273259, the major alleleT of IFI44L rs1333973, the major allele C of CD46 rs4844619, the majorallele C of CD46 rs2466572, the major allele T of CD46 rs2724360, themajor allele G of CD46 rs6657476, the major allele A of CD46 rs4844390,the major allele A of IFI44L rs4650590, the major allele G of IFI44Lrs6693207, the major allele A of IFI44L rs273255, the major allele G ofIFI44L rs273261, the major allele A of IFI44L rs273256, the major alleleA of IFI44L rs273244, the major allele T of LOC101929385 rs11118612, themajor allele C of LOC101929385 rs4844392, the major allele A ofLOC101929385 rs66532523, the major allele G of LOC101929385 rs4844620,the major allele G of intergenic rs2761437, the major allele T ofintergenic rs2796265, the major allele G of intergenic rs2761434, themajor allele T of intergenic rs56075814, the major allele T ofintergenic rs6669384, the major allele T of intergenic rs55935450, themajor allele C of intergenic rs11118668, the major allele T ofintergenic rs1318653, the major allele T of intergenic rs61821293, themajor allele G of intergenic rs273238, the major allele A of intergenicrs12026737, and the minor allele C of CD46 rs11806810 in the sample.

In another aspect, this document features a method for identifying ahuman having cancer as being unlikely to respond to a measlesvirus-based oncolytic treatment. The method comprises, or consistsessentially of, (a) detecting the presence of the minor allele G of CD46rs2724374, the minor allele G of CD46 rs2724384, the minor allele G ofIFI44L rs273259, the minor allele A of IFI44L rs1333973, the minorallele T of CD46 rs4844619, the minor allele A of CD46 rs2466572, theminor allele C of CD46 rs2724360, the minor allele T of CD46 rs6657476,the minor allele G of CD46 rs4844390, the minor allele G of IFI44Lrs4650590, the minor allele A of IFI44L rs6693207, the minor allele T ofIFI44L rs273255, the minor allele A of IFI44L rs273261, the minor alleleC of IFI44L rs273256, the minor allele T of IFI44L rs273244, the minorallele A of LOC101929385 rs11118612, the minor allele G of LOC101929385rs4844392, the minor allele C of LOC101929385 rs66532523, the minorallele A of LOC101929385 rs4844620, the minor allele A of intergenicrs2761437, the minor allele C of intergenic rs2796265, the minor alleleA of intergenic rs2761434, the minor allele C of intergenic rs56075814,the minor allele C of intergenic rs6669384, the minor allele A ofintergenic rs55935450, the minor allele T of intergenic rs11118668, theminor allele C of intergenic rs1318653, the minor allele G of intergenicrs61821293, the minor allele A of intergenic rs273238, the minor alleleC of intergenic rs12026737, or the major allele G of CD46 rs11806810 ina sample obtained from the human, and (b) classifying the human as beingunlikely to respond to the measles virus-based oncolytic treatment. Themethod can comprise detecting the presence of the minor allele G of CD46rs2724374, the minor allele G of CD46 rs2724384, the minor allele G ofIFI44L rs273259, the minor allele A of IFI44L rs1333973, the minorallele T of CD46 rs4844619, the minor allele A of CD46 rs2466572, theminor allele C of CD46 rs2724360, the minor allele T of CD46 rs6657476,the minor allele G of CD46 rs4844390, the minor allele G of IFI44Lrs4650590, the minor allele A of IFI44L rs6693207, the minor allele T ofIFI44L rs273255, the minor allele A of IFI44L rs273261, the minor alleleC of IFI44L rs273256, the minor allele T of IFI44L rs273244, the minorallele A of LOC101929385 rs11118612, the minor allele G of LOC101929385rs4844392, the minor allele C of LOC101929385 rs66532523, the minorallele A of LOC101929385 rs4844620, the minor allele A of intergenicrs2761437, the minor allele C of intergenic rs2796265, the minor alleleA of intergenic rs2761434, the minor allele C of intergenic rs56075814,the minor allele C of intergenic rs6669384, the minor allele A ofintergenic rs55935450, the minor allele T of intergenic rs11118668, theminor allele C of intergenic rs1318653, the minor allele G of intergenicrs61821293, the minor allele A of intergenic rs273238, the minor alleleC of intergenic rs12026737, and the major allele G of CD46 rs11806810 inthe sample.

In another aspect, this document features a method for treating a humanhaving cancer. The method comprises, or consists essentially of, (a)detecting the presence of the minor allele G of CD46 rs2724374, theminor allele G of CD46 rs2724384, the minor allele G of IFI44L rs273259,the minor allele A of IFI44L rs1333973, the minor allele T of CD46rs4844619, the minor allele A of CD46 rs2466572, the minor allele C ofCD46 rs2724360, the minor allele T of CD46 rs6657476, the minor allele Gof CD46 rs4844390, the minor allele G of IFI44L rs4650590, the minorallele A of IFI44L rs6693207, the minor allele T of IFI44L rs273255, theminor allele A of IFI44L rs273261, the minor allele C of IFI44Lrs273256, the minor allele T of IFI44L rs273244, the minor allele A ofLOC101929385 rs11118612, the minor allele G of LOC101929385 rs4844392,the minor allele C of LOC101929385 rs66532523, the minor allele A ofLOC101929385 rs4844620, the minor allele A of intergenic rs2761437, theminor allele C of intergenic rs2796265, the minor allele A of intergenicrs2761434, the minor allele C of intergenic rs56075814, the minor alleleC of intergenic rs6669384, the minor allele A of intergenic rs55935450,the minor allele T of intergenic rs11118668, the minor allele C ofintergenic rs1318653, the minor allele G of intergenic rs61821293, theminor allele A of intergenic rs273238, the minor allele C of intergenicrs12026737, or the major allele G of CD46 rs11806810 in a sampleobtained from the human, and (b) administering a modified measlesvirus-based oncolytic treatment or a non-measles virus-based oncolytictreatment to the human. The method can comprise detecting the presenceof the minor allele G of CD46 rs2724374, the minor allele G of CD46rs2724384, the minor allele G of IFI44L rs273259, the minor allele A ofIFI44L rs1333973, the minor allele T of CD46 rs4844619, the minor alleleA of CD46 rs2466572, the minor allele C of CD46 rs2724360, the minorallele T of CD46 rs6657476, the minor allele G of CD46 rs4844390, theminor allele G of IFI44L rs4650590, the minor allele A of IFI44Lrs6693207, the minor allele T of IFI44L rs273255, the minor allele A ofIFI44L rs273261, the minor allele C of IFI44L rs273256, the minor alleleT of IFI44L rs273244, the minor allele A of LOC101929385 rs11118612, theminor allele G of LOC101929385 rs4844392, the minor allele C ofLOC101929385 rs66532523, the minor allele A of LOC101929385 rs4844620,the minor allele A of intergenic rs2761437, the minor allele C ofintergenic rs2796265, the minor allele A of intergenic rs2761434, theminor allele C of intergenic rs56075814, the minor allele C ofintergenic rs6669384, the minor allele A of intergenic rs55935450, theminor allele T of intergenic rs11118668, the minor allele C ofintergenic rs1318653, the minor allele G of intergenic rs61821293, theminor allele A of intergenic rs273238, the minor allele C of intergenicrs12026737, and the major allele G of CD46 rs11806810 in the sample.

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention pertains. Although methods and materialssimilar or equivalent to those described herein can be used in thepractice or testing of the present invention, suitable methods andmaterials are described below. All publications, patent applications,patents, and other references mentioned herein are incorporated byreference in their entirety. In case of conflict, the presentspecification, including definitions, will control. In addition, thematerials, methods, and examples are illustrative only and not intendedto be limiting.

Other features and advantages of the invention will be apparent from thefollowing detailed description, and from the claims.

DESCRIPTION OF DRAWINGS

FIGS. 1A-1D. Locus zoom plots of the chromosome 1 regions and effects ofSNPs associated with measles-specific neutralizing antibody titers inthe combined cohort. (A and C) Locus zoom plots of the 1q32 (CD46, A)and 1q31.1 (IFI44L, C) regions associated with neutralizing antibodytiter after measles vaccination. On the x-axis, SNPs are plotted bychromosomal location. The left y-axis reflects the association (−log₁₀P-value) with vaccine-induced measles-specific antibody titer, while theright y-axis reflects recombination rates and LD (r² color) of eachplotted SNP with the most significant SNP (designated by a blackdiamond). (B and D) Effect of top two CD46 SNPs (B) and IFI44L SNPs (D)on measles-specific antibody response (effect in the combined cohort ispresented as Turkey box-and-whisker plots). On the x-axis, 0 designatessubjects with homozygous major allele genotype, 1 designatesheterozygous subjects, and 2 designates subjects with homozygous minorallele genotype. On the y-axis, neutralizing antibody titer is presentedas the natural log of the PRMN mIU/mL value. The top (bottom) of the boxindicates the 75th (25th) percentiles, respectively, while the bold linewithin the box indicates the median, and the whiskers indicate 1.5 timesthe IQR (n=2872; reduced to 2818 after excluding subjects with immuneoutcome data that failed QC).

FIGS. 2A-2B. Manhattan and Q-Q plots summary of genome-wide associationstudy associations between SNPs and measles-specific neutralizingantibody titers. (A) Manhattan (left panel) and Q-Q (right panel) plotsfor the combined cohort analysis (n=2872; reduced to 2818 afterexcluding subjects with neutralizing antibody data, that failed QC). (B)Manhattan (left panel) and Q-Q (right panel) plots for the subsetanalysis of subjects of Caucasian ancestry (n=2555; reduced to 2506after excluding subjects with neutralizing antibody data, that failedQC).

FIG. 3. Haplotype block structure of the significant IFI44L and CD46SNPs associated with measles-specific antibody response (combinedsample). The schematic representation and LD block structure of IFI44L(left) and CD46 (right) genetic regions are depicted (significantlyassociated SNPs only). The LD block structure was analyzed usingHaploview software, version 4.2. The r² color scheme is: white (r²=0),shades of grey (0<r²<1), black (r²=1). The numbers report the r² valuemultiplied by 100.

FIG. 4. Manhattan plot summary of genome-wide association studyassociations between SNPs and measles-specific IFNγ ELISPOT response inthe combined cohort (n=2872; reduced to 2618 after excluding subjectswith immune outcome data that failed QC).

FIGS. 5A-5C. Differential exon/isoform CD46 and IFI44L usage. (A)Estimated exon usage in the CD46 gene comparing individuals with atleast one minor allele (G for rs2724374, i.e., all the heterozygoussubjects plus the one homozygous minor allele subject combined, totaln=9) (blue) to individuals that are homozygous major (T for rs2724374)allele, n=19 (red). Even with a relatively small number of subjectspossessing the minor allele genotype, differential exon usage with ahighly significant p-value was observed for the STP exon B (genomic ID207941124-207941168) (p=2.96×10⁻⁷). (B) RT-PCR analysis of common CD46isoforms was performed in PBMCs of rs2724374 homozygous major allelegenotype individuals (n=10) compared to homozygous minor allele genotypeindividuals (n=10) and heterozygous individuals (n=10). The presentedfigure is representative of the patterns observed in all 30 subjects (10subjects per genotype group) with the experiment replicated twice. (C)Estimated exon usage in IFI44L rs1333973/rs273259 homozygous minorallele genotype subjects (A for rs1333973, n=5, blue) vs. homozygousmajor allele subjects (T for rs1333973, n=11, red). The resultsdemonstrate significant per-exon estimates for several IFI44L exons, themost significant being exon 2 (genomic ID 79093591-79094078)(q=2.37×10⁻¹⁵⁰).

FIG. 6. Structure of CD46. The extracellular portion of CD46 consists offour N-glycosylated conserved short consensus repeats SCR1-4 (SCR1 andSCR2 containing binding sites for MV); a STP region that isO-glycosylated (encoded by exons 7, 8 and 9, designated as A, B and C);and a region of unknown function (U), followed by a hydrophobictransmembrane segment (H), basic amino acid anchor (A), and acytoplasmic tail (CYT1 of 16 amino acids if exon 13 is present, or CYT2of 23 amino acids if exon 13 is alternatively spliced). Of the 14 knownCD46 isoforms resulting from alternative splicing, four are commonlyfound in most human tissues and are designated based on the present STPexon/exons and the cytoplasmic tail: BC1 and BC2 (with B and Cexons/domains in the STP and with either CYT1 or CYT2), and C1 and C2(with C exon/domain in the STP and with either CYT1 or CYT2). The effectof CD46 rs2724374 on CD46 isoform prevalence (exon B presence orskipping), interaction between CD46 and MV, and immune responsefollowing measles vaccination is also summarized.

FIGS. 7A-7D. Flexibility of CD46 isoforms and impact on MV-CD46interactions and MV fusion. (A) CD46 is a cell surface receptor affectedby isoform differences. Due in part to its elongated structure, theextracellular domains will naturally exhibit flexibility within thephysiologic environment (represented as rotational blurring of thereference isoform ABC1/ABC2). SCR domain residues are colored in yellow.The modeled segment of CD46 includes the extracellular domains and isshown in cartoon representation. (B) Molecular modeling of theextracellular portion of BC1 (BC2) and C1 (C2) isoforms (the four mostcommon isoforms) through SCR4, followed by generation of mechanics-basedmodels (ANM), indicates a difference in the intrinsic flexibilitybetween the isoforms (see FIG. 8 for details). The amino acids encodedby exons 8-10 are indicated by different colors. Representative motionfrom the ANM models for the BC1 and C1 isoforms are shown by showingmultiple conformational states superimposed. (C) CD46 on the cellsurface interacts with MV-H on the virion surface. Two CD46 moleculesinteracting with a MV-H dimer are depicted. Using ANM, the intrinsicflexibility of the MV-H dimer was quantified. The dominant motion is ananti-correlated twisting or ratcheting of the monomers with respect toone another. Projection the effect of this motion onto the bound CD46molecules is represented by black arrows on each residue. As theC-terminus of CD46 is anchored in the cell membrane, activation of thismotion would require flexibility of the CD46 molecule—flexibility thatmay differ by isoform (panel B). Presented is a second view of themotion rotated 90°, omitting the cartoon representation for clarity—onlythe motion-vectors are shown to emphasize the twisting of the MV-H dimerand its effect on CD46. (D) Proposed molecular mechanism: MV-H and thefusion protein MV-F are normally associated with one another on thevirus surface. Proteins are represented by smoothed molecular surfaces.The encounter complex between CD46 and MV-H leads to MV-Fdisassociation. The disassociation is influenced by the MV-Hconformational change and motion in the context of the CD46-H dimercomplex. The free MV-F undergoes a substantial conformational change,the molecular details of which are not fully resolved, leading tobridging between the virus and target cell. The degree of flexibilityexhibited by CD46 may influence (a) the ease with which the complex mayundergo conformational changes (motion in the context of MV-H-CD46complex) leading to MV-F triggering and fusion, and (b) the rate ofencounter complex formation with MV-H.

FIGS. 8A-8F. CD46 isoforms exhibit different flexibilities, specificallyabout the hinge between the SCR4 and STP domains. (A) Molecularstructure of the full length CD46, zoomed in to emphasize thedifferentially spliced exons. (B) Using the first 3 modes of an ANMmodel, the mobility of each residue was computed. There is increasedmobility for the C1 isoform. (inset) The normal mode frequencies areplotted on a log-log scale and indicate a dramatically lowercollectivity for the C1 isoform. (C) Commute times are computed for eachstructure and show a decrease in C1 relative to BC1. (inset) Examplematrix of commute times from the BC1 isoform with the N-terminus at thetop left and C-terminus bottom right. (D and E) Representative Ca atomswere chosen to define the hinge angle between the exon 6 subdomain, andthe subdomain was comprised of the isoform-specific sequences. Panel Dfor BC1, relatively low mobility about this hinge region is observed(ANM mode 2), while greater flexibility is observed in C1 (ANM mode 2)in E. Representative structures were shown from the ANM modes, deformedto 2A RMSD in both directions and superimposed about the sequencesencoded by the variable exons. (F) Across the first 5 low-frequency ANMmodes, the change in this angle observed when deforming each structureto 2A RMSD in each direction was indicated.

DETAILED DESCRIPTION

This document provides methods and materials involved in using measlesviruses. For example, this document provides methods and materials foridentifying mammals (e.g., humans) likely to respond to standard measlesvirus vaccines or standard measles virus-based oncolytic treatments. Asdescribed herein, a human identified as having the major allele T ofCD46 rs2724374, the major allele A of CD46 rs2724384, the major allele Aof IFI44L rs273259, the major allele T of IFI44L rs1333973, the majorallele C of CD46 rs4844619, the major allele C of CD46 rs2466572, themajor allele T of CD46 rs2724360, the major allele G of CD46 rs6657476,the major allele A of CD46 rs4844390, the major allele A of IFI44Lrs4650590, the major allele G of IFI44L rs6693207, the major allele A ofIFI44L rs273255, the major allele G of IFI44L rs273261, the major alleleA of IFI44L rs273256, the major allele A of IFI44L rs273244, the majorallele T of LOC101929385 rs11118612, the major allele C of LOC101929385rs4844392, the major allele A of LOC101929385 rs66532523, the majorallele G of LOC101929385 rs4844620, the major allele G of intergenicrs2761437, the major allele T of intergenic rs2796265, the major alleleG of intergenic rs2761434, the major allele T of intergenic rs56075814,the major allele T of intergenic rs6669384, the major allele T ofintergenic rs55935450, the major allele C of intergenic rs11118668, themajor allele T of intergenic rs1318653, the major allele T of intergenicrs61821293, the major allele G of intergenic rs273238, the major alleleA of intergenic rs12026737, the minor allele C of CD46 rs11806810, orcombinations thereof can be classified as being a human who is morelikely to favorably respond to standard measles virus vaccinationprotocols and/or measles virus-based therapies (e.g., oncolytic measlesvirus-based therapies). Examples of such therapies and treatmentsinclude, without limitation, those involving the use of measles virusesas a vaccine vector as described elsewhere (Zuniga et al., Vaccine,25(16) 2974 (2007); Reyes-del Valle et al., J. Virol., 83(17):9013-7(2009); Harahap-Carrillo et al., Vaccines (Basel), 3(3):50 (2015);Brandler et al., Vaccine, 28(41):6730 (2010); Ramsauer et al., J.Infect. Dis., 214(suppl 5):S500-S505 (2016); Elsedawy et al., ExpertRev. Vaccines., 12(10):115 (2013); Russell et al., Nat. Biotechnol.,30(7):658 (2012); Lech et al., Expert Rev. Vaccines, 9(11):1275 (2010);Russell et al., Curr. Top. Microbiol. Immunol., 330:21 (2009); Msaouelet al., Expert Opin. Biol. Ther., 13(4):483 (2013); and Msaouel et al.,Curr. Pharm. Biotechnol., 13(9):1732 (2012)). In some cases, humansidentified as having two or more of the major alleles listed in thisparagraph (e.g., homozygous major allele genotype) are more likely tofavorably respond to standard measles virus vaccination protocols and/ormeasles virus-based therapies. In some cases, such identified humans canbe administered a standard measles virus vaccination protocol whenundergoing measles virus vaccination or a measles virus-based therapy.

Examples of standard measles virus vaccination protocols that can beused when vaccinating a human identified as described herein include,without limitation, administering two doses of a measles-containingvaccine in a life time. Any appropriate measles virus-based oncolytictreatment or other measles virus-based therapy/treatment can be usedwhen treating cancer (or other condition) in a human identified as beinga favorable responder as described herein. Examples of measlesvirus-based oncolytic treatments that can be used as described hereininclude, without limitation, those described elsewhere (Elsedawy et al.,Expert Rev. Vaccines., 12(10):115 (2013); Russell et al., Nat.Biotechnol., 30(7):658 (2012); Lech et al., Expert Rev. Vaccines,9(11):1275 (2010); Russell et al., Curr. Top. Microbiol. Immunol.,330:21 (2009); Msaouel et al., Expert Opin. Biol. Ther., 13(4):483(2013); and Msaouel et al., Curr. Pharm. Biotechnol., 13(9):1732(2012)). Measles virus-based oncolytic therapy can be used in a humanidentified as being a favorable responder as described herein.

Any appropriate cancer can be treated using a measles virus-basedoncolytic treatment in a human identified as being a favorable responderas described herein including, without limitation, Hodgkin's disease,Burkitt's lymphoma, multiple myeloma, ovarian cancer, colorectal cancer,breast cancer, lymphoma, leukemia, thyroid cancer, ovarian cancer, livercancer, prostate cancer, mesothelioma, melanoma, renal cell carcinoma,fibrosarcoma, hepatocellular carcinoma, medulloblastoma, head and necksquamous cell cancer, rhabdomyosarcoma, and glioma (see, e.g., Russellet al., Curr. Top. Microbiol. Immunol., 330:213 (2009); Blechacz et al.,Hepatology. 44(6):1465-77 (2006); and Russell et al., Nat. Biotechnol.,30(7):658 (2012).

In some cases, the major allele T of CD46 rs2724374, the major allele Aof CD46 rs2724384, the major allele A of IFI44L rs273259, the majorallele T of IFI44L rs1333973, the major allele C of CD46 rs4844619, themajor allele C of CD46 rs2466572, the major allele T of CD46 rs2724360,the major allele G of CD46 rs6657476, the major allele A of CD46rs4844390, the major allele A of IFI44L rs4650590, the major allele G ofIFI44L rs6693207, the major allele A of IFI44L rs273255, the majorallele G of IFI44L rs273261, the major allele A of IFI44L rs273256, themajor allele A of IFI44L rs273244, the major allele T of LOC101929385rs11118612, the major allele C of LOC101929385 rs4844392, the majorallele A of LOC101929385 rs66532523, the major allele G of LOC101929385rs4844620, the major allele G of intergenic rs2761437, the major alleleT of intergenic rs2796265, the major allele G of intergenic rs2761434,the major allele T of intergenic rs56075814, the major allele T ofintergenic rs6669384, the major allele T of intergenic rs55935450, themajor allele C of intergenic rs11118668, the major allele T ofintergenic rs1318653, the major allele T of intergenic rs61821293, themajor allele G of intergenic rs273238, the major allele A of intergenicrs12026737, and the minor allele C of CD46 rs11806810 can be used incombination to identify a human who is more likely to favorably respondto standard measles virus vaccination protocols and/or measlesvirus-based therapies (e.g., oncolytic measles virus-based therapies).

This document also provides methods and materials for identifyingmammals (e.g., humans) unlikely to respond to standard measles virusvaccines or standard measles virus-based oncolytic treatments. Asdescribed herein, a human identified as having the minor allele G ofCD46 rs2724374, the minor allele G of CD46 rs2724384, the minor allele Gof IFI44L rs273259, the minor allele A of IFI44L rs1333973, the minorallele T of CD46 rs4844619, the minor allele A of CD46 rs2466572, theminor allele C of CD46 rs2724360, the minor allele T of CD46 rs6657476,the minor allele G of CD46 rs4844390, the minor allele G of IFI44Lrs4650590, the minor allele A of IFI44L rs6693207, the minor allele T ofIFI44L rs273255, the minor allele A of IFI44L rs273261, the minor alleleC of IFI44L rs273256, the minor allele T of IFI44L rs273244, the minorallele A of LOC101929385 rs11118612, the minor allele G of LOC101929385rs4844392, the minor allele C of LOC101929385 rs66532523, the minorallele A of LOC101929385 rs4844620, the minor allele A of intergenicrs2761437, the minor allele C of intergenic rs2796265, the minor alleleA of intergenic rs2761434, the minor allele C of intergenic rs56075814,the minor allele C of intergenic rs6669384, the minor allele A ofintergenic rs55935450, the minor allele T of intergenic rs11118668, theminor allele C of intergenic rs1318653, the minor allele G of intergenicrs61821293, the minor allele A of intergenic rs273238, the minor alleleC of intergenic rs12026737, the major allele G of CD46 rs11806810, orcombinations thereof can be classified as being a human who is lesslikely to favorably respond (and/or more likely to not favorablyrespond) to standard measles virus vaccination protocols and/or measlesvirus-based therapies (e.g., oncolytic measles virus-based therapies)such as those therapies/treatments using measles virus as a vaccinevector as described elsewhere (Zuniga et al., Vaccine, 25(16) 2974(2007); Reyes-del Valle et al., J. Virol., 83(17):9013-7 (2009);Harahap-Carrillo et al., Vaccines (Basel), 3(3):50 (2015); Brandler etal., Vaccine, 28(41):6730 (2010); Ramsauer et al., J. Infect. Dis.,214(suppl 5):S500-S505 (2016); Elsedawy et al., Expert Rev. Vaccines.,12(10):115 (2013); Russell et al., Nat. Biotechnol., 30(7):658 (2012);Lech et al., Expert Rev. Vaccines, 9(11):1275 (2010); Russell et al.,Curr. Top. Microbiol. Immunol., 330:21 (2009); Msaouel et al., ExpertOpin. Biol. Ther., 13(4):483 (2013); and Msaouel et al., Curr. Pharm.Biotechnol., 13(9):1732 (2012)). In some cases, humans identified ashaving two of the minor alleles listed in this paragraph (e.g.,homozygous minor allele genotype) can be less likely to favorablyrespond (e.g., more likely to not favorably respond) to standard measlesvirus vaccination protocols and/or measles virus-based therapies. Insome cases, such identified humans can be administered an enhancedmeasles virus vaccination protocol when undergoing measles virusvaccination or a modified measles virus-based therapy (or non-measlesvirus-based therapy or oncolytic treatment in cancer) when being treatedfor cancer or other conditions. Examples of enhanced measles virusvaccination protocols that can be used when vaccinating a humanidentified as being unlikely to respond to standard measles virusvaccination protocols as described herein include, without limitation,increased dosage or number of doses, different route of immunization(e.g., intranasal, where the virus could preferentially use otherreceptors), modified vaccine formulation (e.g., adjuvants boostingsurface expression of CD46 and/or upregulation of IFI44L), modifiedmeasles vaccine virus with equivalent or enhanced ability to infect theCD46 variant expressed by low responders or modified measles vaccinevirus using exclusively other natural entry receptors such as SLAM orNectin-4 (PVRL4) or measles virus artificially retargeted to othercellular ligands/receptors as described elsewhere (Aref et al., Viruses,8(10) pii:E294 (2016); and Lin and Richardson, Viruses, 8(9) pii:E250(2016)). Any appropriate modified measles virus-based therapy (orvirus-based oncolytic therapy in the case of malignancies) ornon-measles virus-based therapy can be used when treating cancer orother conditions in a human identified as being less likely to respondto measles virus-based therapy as described herein. Examples of measlesvirus-based oncolytic treatments include, without limitation, those inadvanced stage of clinical research and undergoing clinical trials (see,e.g., Elsedawy et al., Expert Rev. Vaccines., 12(10):115 (2013); Russellet al., Nat. Biotechnol., 30(7):658 (2012); Lech et al., Expert Rev.Vaccines, 9(11):1275 (2010); Russell et al., Curr. Top. Microbiol.Immunol., 330:21 (2009); Msaouel et al., Expert Opin. Biol. Ther.,13(4):483 (2013); and Msaouel et al., Curr. Pharm. Biotechnol.,13(9):1732 (2012)). Any appropriate cancer can be treated using amodified and/or enhanced measles virus-based oncolytic treatment ornon-measles virus-based oncolytic treatment in a human identified asbeing less likely to respond to measles virus-based therapy/treatment asdescribed herein including, without limitation, Hodgkin's disease,Burkitt's lymphoma, multiple myeloma, ovarian cancer, colorectal cancer,breast cancer, lymphoma, leukemia, thyroid cancer, ovarian cancer, livercancer, prostate cancer, mesothelioma, melanoma, renal cell carcinoma,fibrosarcoma, hepatocellular carcinoma, medulloblastoma, head and necksquamous cell cancer, fibrosarcoma, rhabsomyosarcoma, and glioma.

In some cases, the minor allele G of CD46 rs2724374, the minor allele Gof CD46 rs2724384, the minor allele G of IFI44L rs273259, the minorallele A of IFI44L rs1333973, the minor allele T of CD46 rs4844619, theminor allele A of CD46 rs2466572, the minor allele C of CD46 rs2724360,the minor allele T of CD46 rs6657476, the minor allele G of CD46rs4844390, the minor allele G of IFI44L rs4650590, the minor allele A ofIFI44L rs6693207, the minor allele T of IFI44L rs273255, the minorallele A of IFI44L rs273261, the minor allele C of IFI44L rs273256, theminor allele T of IFI44L rs273244, the minor allele A of LOC101929385rs11118612, the minor allele G of LOC101929385 rs4844392, the minorallele C of LOC101929385 rs66532523, the minor allele A of LOC101929385rs4844620, the minor allele A of intergenic rs2761437, the minor alleleC of intergenic rs2796265, the minor allele A of intergenic rs2761434,the minor allele C of intergenic rs56075814, the minor allele C ofintergenic rs6669384, the minor allele A of intergenic rs55935450, theminor allele T of intergenic rs11118668, the minor allele C ofintergenic rs1318653, the minor allele G of intergenic rs61821293, theminor allele A of intergenic rs273238, the minor allele C of intergenicrs12026737, and the major allele G of CD46 rs11806810 can be used incombination to identify a human who is less likely to favorably respond(and/or more likely to not favorably respond) to respond to standardmeasles virus vaccination protocols and/or measles virus-basedtherapies.

Any appropriate method can be used to determine the presence or absenceof particular alleles for the SNP positions provided herein. Forexample, nucleic acid sequencing techniques such as Sanger sequencing ornext generation sequencing can be used to identify which nucleotides arepresent at the SNP locations identified herein. In some cases, SNPdetection techniques can be used to identify which nucleotides arepresent at the SNP locations identified herein.

The invention will be further described in the following examples, whichdo not limit the scope of the invention described in the claims.

EXAMPLES Example 1—Genome-Wide Associations of CD46 and IFI44L GeneticVariants with Neutralizing Antibody Response to Measles Vaccine StudySubjects

A large sample of 3,191 healthy children, older adolescents, and healthyadults (age 11 to 40 years) consisting of three independent cohorts wereanalyzed: a Rochester cohort (n=1,062); a San Diego cohort (n=1,071);and a US cohort (n=1,058). The demographic and clinical characteristicsof these cohorts are described elsewhere (Haralambieva et al., Vaccine,29:7883-7895 (2011); Haralambieva et al., Vaccine, 29:8988-8997 (2011);Kennedy et al., Vaccine, 30:2159-2167 (2012); Kennedy et al., HumanGenetics, 131:1433-1451 (2012); Kennedy et al., Human Genetics,131:1403-1421 (2012); Lambert et al., J. Infect. Dis., 211:898-905(2015); Ovsyannikova et al., Human Heredity, 72:206-223 (2011);Ovsyannikova et al., Human Genetics, 130:547-561 (2011); andOvsyannikova et al., Vaccine, 30:2146-2152 (2012)).

The Rochester cohort comprised 1,062 individuals enrolled into threeage-stratified cohorts of healthy, school-age children and young adultsfrom all socioeconomic strata in Rochester, Minn., recruited between2001-2009. Each subject had written records of having received two dosesof MMR vaccine. Of the 1,062 individuals for this study, 982 (93%) weresuccessfully genotyped and assayed for immune outcomes.

The San Diego cohort consisted of 1,071 healthy older adolescents andhealthy adults (age 18 to 40 years) from armed forces personnel in SanDiego, Calif., enrolled by the US Naval Health Research Center (NHRC)between 2005-2006. The US cohort consisted of an additional 1,058healthy older adolescents and healthy adults recruited from the US armedforces, enrolled between 2010-2011. Of the 1,071 and 1,058 subjectsrecruited into this study as the San Diego or US cohort (respectively),882 (82%) subjects for the San Diego cohort and 1,008 (95%) subjects forthe US cohort had provided consent for use of their samples/data inother studies, and were successfully genotyped and assayed formeasles-specific immune outcomes for this study.

Genotyping and Immune Outcomes

The genome-wide SNP typing was performed using the Infinium Omni 1M-QuadSNP array (Illumina; San Diego, Calif.) for the Rochester cohort,Illumina Human Omni2.5-8 BeadChip array for the US cohort, and IlluminaInfinium HumanHap550v3_A or HumanHap650Yv3 BeadChip arrays for the SanDiego cohort. Measles-specific neutralizing antibody and cytokineresponses were quantified using a fluorescence-based plaque reductionmicroneutralization assay (PRMN) and ELISPOT/ELISA assays as describedelsewhere (Haralambieva et al., Vaccine, 29:4485-4491 (2011)). Thehumoral immune response phenotype, the 50% end-point titer (NeutralizingDose, ND50), was calculated using Karber's formula and transformed intomIU/mL (using the 3rd WHO international measles antibody standard), asdescribed elsewhere (Haralambieva et al., Vaccine, 29:4485-4491 (2011)).The variability of the PRMN assay, calculated as a coefficient ofvariation (CV) based on the log-transformed ND50 values of the third WHOstandard, was 5.7%, as described elsewhere (Haralambieva et al.,Vaccine, 29:4485-4491 (2011)).

Briefly, DNA was extracted from each subject's blood specimen using theGentra Puregene Blood kit (Gentra Systems Inc.; Minneapolis, Minn.) andquantified by Picogreen (Molecular Probes; Carlsbad, Calif.). Thegenome-wide SNP typing was performed using the Infinium Omni 1M-Quad SNParray (Illumina; San Diego, Calif.) for the Rochester cohort, IlluminaHuman Omni2.5-8 BeadChip array for the US cohort, and Illumina InfiniumHumanHap550v3_A or HumanHap650Yv3 BeadChip arrays for the San Diegocohort. DNA samples underwent amplification, fragmentation, andhybridization onto each BeadChip, which were imaged on an IlluminaBeadArray reader. Genotype calls based on clustering of the rawintensity data were made using BeadStudio 2 software.

For the 758 subjects in the San Diego cohort with the Illumina 550 arraygenotyping data, 54 subjects were removed due to high SNP missing rates(more than 5% of their SNPs missing). There were 561,303 unique measuredSNPs, of which 508,199 SNPs passed QC. For the 313 subjects in the SanDiego cohort with the Illumina 650 array genotyping data, 13 subjectswere removed due to high SNP missing rates. There were 660,755 uniquemeasured SNPs, of which 630,240 passed QC. In addition, subjects werefurther excluded from the San Diego cohort if not of Caucasian orAfrican-American ancestry (determined by STRUCTURE), or if they weremissing values for covariates used in the analysis. This resulted in atotal of 882 subjects from this cohort used in the study (718 Caucasiansand 164 African-Americans, see Table 1). For the 1,058 subjects in theUS cohort with the Illumina Omni 2.5 array genotyping data, there were2,376,105 measured SNPs, of which 2,116,447 passed QC. Subjects wereexcluded from the US cohort if not of Caucasian or African-Americanancestry as determined by STRUCTURE, or had high SNP missing rates, orif values for covariates were missing; this resulted in a total of 1,008subjects (895 Caucasians and 113 African Americans, Table 1). For the1,062 subjects in the Rochester cohort with valid data, 10 subjects wereremoved due to high SNP missing rates. Subjects were further excludedfrom the cohort if not of Caucasian or African-American ancestrydetermined by STRUCTURE, or if values for covariates were missing; thisresulted in a total of 982 subjects (942 Caucasians and 40 AfricanAmericans, Table 1). On the Omni 1 genotyping array, there were1,134,514 unique measured SNPs, of which 887,889 passed QC.

TABLE 1 Demographic and immune characterization of the study populationAfrican American^(e) Caucasian^(e) Total (n = 317) (n = 2555) (n = 2872)P-value Neutralizing Ab titer^(a) <0.001^(f) N missing (failed assay QC) 5  49  54 Mean (SD^(c)) 2065 (2821) 1271 (1652) 1359 (1835) Median(IQR^(d)) 1180 (550, 2632) 803 (383, 1607) 845 (394, 1683) IFNγ ELISPOTresponse^(b) 0.427^(f) N missing (failed assay QC)  26 228 254 Mean(SD^(c)) 24.4 (26) 25.2 (32) 25.1 (31.4) Median (IQR^(d)) 15 (7, 34.5)15 (6, 32.5) 15 (6, 32.7) Gender/sex 0.082^(g) Female 73 (23%) 707(27.7%) 780 (27.2%) Male 244 (77%) 1848 (72.3%) 2092 (72.8%) Race(self-declared) NA^(h) White 0 (0%) 2206 (86.3%) 2206 (76.8%) Black orAfrican American 302 (95.3%) 38 (1.49%) 340 (11.8%) AmericanIndian/Alaska Native 0 (0%) 29 (1.14%) 29 (1.01%) Asian/Hawaiian/PacificIslander 1 (0.315%) 19 (0.744%) 20 (0.696%) Multiple 9 (2.84%) 100(3.91%) 109 (3.8%) Other 4 (1.26%) 119 (4.66%) 123 (4.28%) Unknown 1(0.315%) 44 (1.72%) 45 (1.57%) Ethnicity (self-declared) <0.001^(g)Hispanic/Latino 13 (4.1%) 387 (15.1%) 400 (13.9%) Not Hispanic/Latino285 (89.9%) 2137 (83.6%) 2422 (84.3%) Unknown 19 (5.99%) 31 (1.21%) 50(1.74%) Age at enrollment (years) <0.001^(f) Number missing  49 196 245Mean (SD^(c)) 24.5 (5.97) 21.1 (6.06) 21.4 (6.14) Median (IQR^(d)) 24(21, 28) 22 (16, 25) 22 (16, 25) Age at last vaccination (years)<0.001^(f) Number missing 107 577 684 Mean (SD^(c)) 19.8 (7.97) 16.1(8.38) 16.4 (8.41) Median (IQR^(d)) 20 (18, 24) 18 (10, 22) 18 (11, 23)Time from last vaccination to 0.031^(f) enrollment (years) Numbermissing 107 577 684 Mean (SD^(c)) 3.7 (3.85) 4.0 (3.43) 4.0 (3.47)Median (IQR^(d)) 2.6 (0.04, 5.5) 3.5 (0.03, 6.4) 3.4 (0.03, 6.4) Cohort<0.001^(g) Rochester 40 (12.6%) 942 (36.9%) 982 (34.2%) San Diego 164(51.7%) 718 (28.1%) 882 (30.7%) US 113 (35.6%) 895 (35%) 1008 (35.1%)^(a)Neutralizing antibody titer in mIU/mL, measured by the plaquereduction microneutralization assay (PRMN) ^(b)IFNγ-positivespot-forming units (SFUs) per 2 × 10⁵ cells (mean of measlesvirus-specific stimulated response, measured in triplicate, minus themean unstimulated response, also measured in triplicate). ^(c)StandardDeviation. ^(d)IQR, inter-quartile range with 25% and 75% quartiles^(e)Genetically classified into African American or Caucasian ancestrygroup based on STRUCTURE (see Methods) ^(f)Kruskal-Wallis Rank Test^(g)Fisher's Exact Test ^(h)Not applicableNext Generation Sequencing (mRNA-Seq)

Libraries were generated from total RNA (extracted from PBMCs of 30subjects) using Illumina's mRNA TruSeq (vi) kit and sequenced (pairedend sequencing) on an Illumina HiSeq 2000 (Illumina; San Diego, Calif.)with Illumina's TruSeq Cluster kit (v3-cBot-HS) and 51 Cycle IlluminaTruSeq SBS Sequencing Kit (v3), as described elsewhere (Haralambieva etal., PLos ONE, 11:e0160970 (2016)).

Briefly, cryopreserved PBMCs from 30 Rochester cohort subjects (selectedfor an mRNA-Seq transcriptome profiling, based on their neutralizingantibody titers (15 highest and 15 lowest antibody responders) after twodoses of MMR vaccine) were thawed and stimulated with live Edmonstonmeasles virus (MV) at a multiplicity of infection (MOI) of 0.5 for 24hours (for each subject, an aliquot of the cells was left unstimulated).The samples were randomly allocated to flow cells and lanes, balancingover the immune response and stimulation status.

Cells were stabilized with RNAprotect cell reagent (Qiagen) and totalRNA was extracted using RNeasy Plus mini kit (Qiagen). Quality andquantity of RNA was determined by Nanodrop spectrophotometry (ThermoFisher Scientific). Libraries were generated using Illumina's mRNATruSeq (v1) kit and sequenced (paired end sequencing) on an IlluminaHiSeq 2000 (Illumina; San Diego, Calif.) with Illumina's TruSeq Clusterkit (v3-cBot-HS) and 51 Cycle Illumina TruSeq SBS Sequencing Kit (v3).The sequencing reads were aligned to the human genome build 37.1 usingTopHat (1.3.3) and Bowtie (0.12.7). Gene counts were performed usingHTSeq (0.5.3p3), while BEDTools software (2.7.1) was used to mapnormalized read count to individual exons (Langmead et al., GenomeBiol., 10:R25 (2009); Quinlan et al., Bioinformatics, 26:841-2 (2010);Trapnell et al., Bioinformatics, 25:1105-11 (2009); and Anders et al.,Bioinformatics, 31:166-9 (2015)).

RT-PCR

One-Step RT-PCR system with Platinum Taq® DNA polymerase (Invitrogen,Carlsbad, Calif.) and primers allowing CD46 isoform/isoformsdiscrimination were used as described elsewhere (Wang et al., J.Immunol., 164:1839-1846 (2000)). Briefly, total RNA was extracted fromPBMCs of 30 subjects (10 CD46 rs2724374 homozygous major allele genotypesubjects, 10 rs2724374 homozygous minor allele genotype subjects and 10heterozygous subjects) using RNAprotect cell reagent and the RNAeasyPlus Mini kit (Qiagen, Valencia, Calif.). RT-PCR analysis of CD46isoforms was performed with the SuperScript One-Step RT-PCR system withPlatinum Taq DNA polymerase (Invitrogen, Carlsbad, Calif.), as describedelsewhere (Wang et al., J. Immunol., 164:1839-1846 (2000)) using the 5′CD46 SCR4 primer GTGGTCAAATGTCGATTTCCAGTAGTCG (SEQ ID NO:1) and the 3′untranslated region primer CAAGCCACATTGCAATATTAGCTAAGCCACA (SEQ IDNO:2), allowing CD46 isoform/isoforms discrimination/separation on a 3%agarose gel.

Immune Outcome Phenotyping

The immune outcome assays described herein were similar or identical tothose described elsewhere (Kennedy et al., Vaccine, 30:2159-2167 (2012);Ovsyannikova et al., Human Genetics, 130:547-561 (2011); Ovsyannikova etal., Human Heredity, 72:206-223 (2011); Haralambieva et al., Vaccine,29:8988-8997 (2011); Haralambieva et al., Vaccine, 29:7883-7895 (2011);Ovsyannikova et al., Vaccine, 30:4182-4189 (2012); Haralambieva et al.,Vaccine, 29:4485-4491 (2011); and Ovsyannikova et al., Human Genetics,133:1083-92 (2014)).

Neutralizing Antibody Assay

Measles-specific neutralizing antibody titers were quantified using ahigh-throughput, fluorescence-based plaque reduction microneutralizationassay (PRMN), using a recombinant GFP-expressing measles virus asdescribed elsewhere (Ovsyannikova et al., Human Heredity, 72:206-223(2011); Haralambieva et al., Vaccine, 29:8988-8997 (2011); Haralambievaet al., Vaccine, 29:7883-7895 (2011); Ovsyannikova et al., Vaccine,30:4182-4189 (2012); Haralambieva et al., Vaccine, 29:4485-4491 (2011);and Ovsyannikova et al., Human Genetics, 133:1083-92 (2014)). The plateswere scanned and counted on an automated Olympus IX71 Fluorescentmicroscope using the Image-Pro Plus Software Version 6.3(MediaCybernetics). The 50% end-point titer (Neutralizing Doze, ND50)was calculated automatically using Karber's formula, and transformedinto mIU/mL (using the 3rd WHO international anti-measles antibodystandard), as described elsewhere (Ovsyannikova et al., Human Heredity,72:206-223 (2011); Haralambieva et al., Vaccine, 29:8988-8997 (2011);Haralambieva et al., Vaccine, 29:7883-7895 (2011); Ovsyannikova et al.,Vaccine, 30:4182-4189 (2012); Haralambieva et al., Vaccine, 29:4485-4491(2011); and Ovsyannikova et al., Human Genetics, 133:1083-92 (2014)).The variability of the PRMN assay, calculated as a coefficient ofvariation (CV) based on the log-transformed ND50 values of the third WHOstandard, was 5.7% (Haralambieva et al., Vaccine, 29:4485-4491 (2011)).

IFNγ ELISPOT Assay

Measles-specific cellular immunity was quantified using commercial HumanIFNγ ELISPOT kits (R&D Systems; Minneapolis, Minn.) to measure thenumber of MV-specific IFNγ-producing cells, according to themanufacturer's instructions and as described elsewhere (Ovsyannikova etal., Pharmacogenet. Genomics, 22:20-31 (2012)). Subjects' peripheralblood mononuclear cells/PBMCs were stimulated (or, alternatively,unstimulated) in triplicate with the Edmonston strain of MV (MOI=0.5),and developed the reaction after 42 hours incubation at 37° C., in 5%CO₂. PHA (5 μg/mL) was used as a positive control. All plates werescanned and analyzed using the same counting parameters on an ImmunoSpotS4 Pro Analyzer (Cellular Technology Ltd.; Cleveland, Ohio) usingImmunoSpot version 4.0 software (Cellular Technology Ltd.). The ELISPOTresponse was presented in spot-forming units (SFUs) per 2×10⁵ cells. Theintraclass correlation coefficients, comparing multiple observations persample (stimulated and unstimulated condition), was 0.94 for thestimulated values and 0.85 for the unstimulated values, indicating lowassay variability.

Measles-Specific Secreted Cytokines

Secreted cytokines (IL-2, IL-6; IL-10; TNFα, IFNγ, IFNα, and IFNλ1) werequantified in PBMC cultures after in vitro stimulation with live MV, asdescribed elsewhere (Ovsyannikova et al., Human Heredity, 72:206-223(2011); Haralambieva et al., Vaccine, 29:8988-8997 (2011); andHaralambieva et al., Vaccine, 29:7883-7895 (2011)).

Statistical Methods GWAS Analysis

To achieve greatest power to detect SNPs associated withmeasles-specific immune response phenotypes, data were pooled acrossgenotyping platforms and the three cohorts. To perform the pooledanalyses, the effects of potentially confounding factors that varyacross ancestry/platform/cohort strata were first accounted for. Afterthoroughly evaluating the quality of the genotype data, the genetic datawere used to define major ancestry groups. Eigenvectors within eachancestry group were then estimated to account for the effects ofpopulation stratification within ancestry groups. Because the largestancestry groups were Caucasian and African-American, pooled analysis wasrestricted to these groups. After accounting for populationstratification, the covariates that were available within each of theancestry-platform-cohort strata were evaluated to determine if thecovariates were associated with the phenotype, in order to regress outthe effects of potential confounding factors. This produced residuals(adjusted traits) that were then used for the GWAS analyses. The immuneresponse trait measles-specific IFNγ ELISPOT, as well asmeasles-specific secreted cytokines, were transformed by normalquantiles of the difference of the mean stimulated and mean unstimulatedvalues. The immune response trait neutralizing antibody titer wastransformed as the natural log of the PRMN mIU/mL value.

Genotype Quality Control and Imputation

Genotype quality control prior to imputation was conducted separatelyfor four strata: subjects in the San Diego cohort with the Illumina 550array genotyping data; subjects in the San Diego cohort with theIllumina 650 array genotyping data; subjects in the US cohort with theOmni 2.5 array genotyping data; and subjects in the Rochester cohortwith the Omni 1M-Quad array genotyping data. SNPs on the Y chromosomeand mitochondria were removed, and SNPs were eliminated if they weremonomorphic or had a missing rate of 1% (5% for the HumanHap550/650arrays) or more. Subjects were eliminated if they had more than 5% oftheir SNPs missing (for the HumanHap550/650 arrays) or more than 1%missing (for the Omni 2.5 and Omni 1M-Quad arrays). The 1000 Genomescosmopolitan samples (African, AFR; AMR; Asian, ASN; European, EUR) wereused as a reference for imputation and were based on Build 37. SNPs thatcould not be converted to Build 37, or mapped to more than one position,or could not have their alleles verified for the forward strand, wereeliminated. The reference genome was then filtered to include only thoseSNPs with a minor allele frequency (MAF) greater than 0.005. The datawere then phased using SHAPEIT (Delaneau et al., Nat. Methods, 10:5-6(2013)) and imputed via IMPUTE2 (Howie et al., PLoS Genet., 5:e1000529(2009)). SNPs with an imputation dosage allele r2 of at least 0.3, and aMAF of at least 0.01, were used in the pooled analyses.

Genetic Ancestry and Population Stratification

Genetic data were used to assign ancestry groups (African, Caucasian, orAsian) for individuals using the STRUCTURE software (Pritchard et al.,Genetics, 155:945-959 (2000)), and using the 1000 Genomes data as areference. These estimates were done within cohort and platform (SanDiego/550, San Diego/650, US/Omni 2.5, Rochester/Omni 1). Others(Novembre et al., Nature, 456:98-101 (2008)) have shown that it isnecessary to perform pruning of the SNPs to be used for eigenvectors inorder to avoid having sample eigenvectors that are determined by smallclusters of SNPs at specific locations, such as the lactose intolerancegene, or polymorphic inversion regions. Therefore, the SNPs used forSTRUCTURE and for eigenvectors were selected by LD pruning from aninitial pool consisting of all autosomal SNPs with the followingfilters: SNPs with a minor allele frequency (MAF)<5% were excluded;influential SNPs were removed (according to the following chromosomeregions: chromosome 8 [bp 1-12700000]; chromosome 2 [bp129900001-136800000, 5700000-33500000]; chromosome 4 [bp0900001-44900000]); correlation (r2) pruning was used to subset touncorrelated SNPs. SNPs passing these selection criteria were input toSTRUCTURE (Pritchard et al., Genetics, 155:945-959 (2000)) to makeancestry “triangle” plots that depict the admixture proportions ofancestry groups for each subject. Subjects were classified into majorancestry groups based on the largest estimated STRUCTURE ancestryproportion.

Eigenvectors were estimated within ancestry groups and platform stratafor refined control of population stratification. For this step, SNPswith a MAF<0.01 were excluded, SNPs with a HWE p-value<0.001 wereexcluded, INDELS were removed, and pruning according to varianceinflation factors was used. These data were then used with smartPCA toproduce a set of eigenvectors using the normalization formulas of Priceet al. (Nature Genetics, 38:904-909 (2006)) following the procedures ofEIGENSTRAT. Tracy-Widom statistics were computed to include eigenvectorsas potential for adjusting covariates if they had a p-value<0.05.

Selection of Covariates to Adjust for Potential Confounders

To remove the effects of potential confounders so that the cohorts couldbe combined, a screen for potential confounders relevant to eachancestry group and cohort was performed. The immune response traitmeasles-specific IFNγ ELISPOT, as well as the measles-specific secretedcytokines, were transformed by normal quantiles of the difference of themean stimulated and mean unstimulated values. Neutralizing antibodytiter was transformed as the natural log of the PRMN mIU/mL value.Possible confounders were screened for their association with the traitusing the following steps. Any categorical variable with a very largenumber of categories was binned using hierarchical clustering. This wasachieved by using hierarchical clustering on the estimated regressioncoefficients for the different categories, binning categories withsimilar regression coefficients. All categorical variables were coded asdummy variables such that the most common category was used as baseline.Variables that were marginally associated with the trait withp-value<0.1 were then included in backwards selection with a p-valuethreshold of 0.1. This somewhat liberal threshold achieved the goal ofcontrolling for potential confounding covariates. Residuals from thefinal “covariate models” were then used as the primary adjusted traitsfor GWAS analyses.

GWAS Pooled Analysis

The adjusted traits for IFNγ ELISPOT and neutralizing antibody werepooled over the three cohorts and genotype platforms to perform thepooled GWAS analysis. To pool the genotypes, the genotypes that wereimputed separately within each platform were used. To analyze Caucasianand African-American ancestry together, a linear regression model thatincluded a cohort indicator, ancestry indicator, dose of minor allele,and interaction of ancestry with dose of minor allele was used. Thisfull model was compared with a reduced model that included a cohortindicator and ancestry indicator. The full and reduced models were usedto create a likelihood ratio test for the effect of a SNP, allowing forthe possible interaction of the SNP with ancestry, resulting in a testwith two degrees of freedom (df). To test for the effect of a SNP withinan ancestry group, a cohort indicator was only used as an adjustingfactor, resulting in a test with one df for the SNP effect. Themeasles-specific secreted cytokines were only measured in the Rochestercohort, so the resulting test for SNP effects was based on a one dfstatistic. All reported p-values are two-sided. To control for multipletesting, the standard p-value<5.0×10⁻⁸ was used (Manolio, New Engl. J.Med., 363:166-76 (2010); and Pe′er et al., Genetic Epidemiology,32:381-5 (2008)) to determine genome-wide statistical significance.Statistical analyses were performed with the R 3.2.0 statisticalsoftware and PLINK (Purcell et al., Am. J. Hum. Genet., 81:559-575(2007)).

Analysis of mRNA-Seq Data for Differential Exon Usage

Evidence of differential exon usage in the CD46 and IFI44L genes wastested for using the method of Anders et al., implemented in the DEXSeqpackage (version 1.16.10) in the R programing language (version 3.2.3)(Anders et al., Genome Res., 22:2008-17 (2012)). This method utilizedgeneralized linear models (GLM) fitting per-gene negative binomialmodels. For the full model, main effects for the sample, exon, and aninteraction between the exon and allele state/genotype (subjects'homozygous minor allele compared to heterozygous and homozygous majorallele) were included. The likelihood estimate from the full model wascompared to the likelihood from the model with the main effects to testthe hypothesis for differential exon usage between the differentgenotypes/allele states. A significant test for a given exon providesevidence of differential exon usage (i.e., an alternative splicing eventto produce different transcripts/isoforms). The per-exon estimates ofthe dispersion for the negative binomial GLMs were calculated using theCox-Reid method (Anders et al., Genome Res., 22:2008-17 (2012); Cox andReid, J. Royal Stat. Soc. Ser. B Methodol., 49:1-39 (1987); and McCarthyet al., Nucleic Acids Res., 40:4288-97 (2012)) applied to all of theobserved exons from the experiment based on the full model. To limit therisk of false discovery, the analyses of differential exon usage werelimited to the CD46 (n=14 exons) and IFI44L (n=9 exons) genes. Themethod of Benjamini and Hochberg was used to control the false discoveryrate, and the adjusted p-values were reported as q-values (Benjamini andHochberg, J Royal Stat. Soc. Series B, 57:289-300 (1995)). mRNA-Seqpaired-end sequencing data on 28 subjects (selected based on theextremes of the distribution of the antibody response, 14 high and 14low antibody responders) was used to test the hypothesis of differentialexon usage (exon expression) between different genotypes of interest(for CD46 rs2724374 and for IFI44L rs1333973/rs273259).

Molecular Modeling

In order to evaluate the effect of differential splicing on the dynamicsof the CD46 molecular structure, homology models (Roy et al., NatureProtocols, 5:725-38 (2010)) were generated of the extracellular domains(SCR1-4 and STP domains) for each isoform and analyzed each usingAnisotropic Network Models (ANMs) (Atilgan et al., Biophysical J.,80:505-15 (2001); Chennubhotla and Bahar, PLoS Computational Biol.,3:1716-26 (2007); and Yang et al., PNAS, 106:12347-52 (2009)) usingmultiple templates. The crystal structure of MV-H and its interactionsbetween with CD46 and MV-H were taken modeled from using the crystalstructure PDB 3INB (Santiago et al., Nature Struct. Mol. Biol., 17:124-9(2010)) as a template wherein dimeric MV-H is bound symmetrically by theSCR1 and SCR2 domains of two CD46 molecules.

No full-length structure of CD46 exists, but partial structures of theextracellular domains have been solved. These cover the sequencesencoded by the first six exons of the gene. Available experimentalstructures include the co-crystal structure between CD46 SCR1-4 and theadenovirus type 11 knob (3o8e (Persson et al., PLoS Pathogens,6:e1001122 (2010)), and a co-crystal structure of CD46 SCR1-2 bound tothe MV-H globular head domain dimer (3inb; Santiago et al., NatureStruct. Mol. Biol., 17:124-9 (2010)). Computationally determined modelshave also been deposited in MODBASE (Pieper et al., Nucl. Acids Res.,32:D217-22 (2004)). Homology models of the extracellular domains (SCR1-4and STP domains) of ABC1, BC1, and C1 isoforms of CD46 (identical toABC2, BC2, and C2, respectively) were generated using I-TASSER (Roy etal., Nature Protocols, 5:725-38 (2010)) and compared them to the MODBASEmodels and available crystal structures, in order to evaluate modelquality and consistency.

In order to evaluate the effect of differential splicing on the dynamicsof the CD46 structure, Anisotropic Network Models (ANMs) (Zimmermann etal., BMC Bioinformatics, 12:264 (2011); and Atilgan et al., Biophys. 1,80:505-15 (2001)) were generated using a distance-dependent interactionstrength (Yang et al., PNAS, 106:12347-52 (2009)). Models were evaluatedusing computed Mean Squared Fluctuations as a per-residue measure ofmobility, commute time (Chennubhotla and Bahar, PLoS Comput. Biol.,3:1716-26 (2007)) as a measure of efficiency with which informationpasses through the structure, and angle monitors to evaluate overalldomain-domain orientations. The motions computed by ANM aretheoretically local (small-scale), but often correlate strongly withlarge-scale functional motions. Thus, the functional magnitudes of ANMmotions were not intrinsically defined. Therefore, each structure wasdeformed to 2A RMSD in each direction of a given mode as a consistentand realistic extent of motion.

The crystal structure of the MV-H head domain dimer and its interactionswith CD46 were taken from PDB 3INB (Santiago et al., Nature Struct. Mol.Biol., 17:124-9 (2010)), and its dynamics was modeled using ANM. Motionsof bound CD46 molecules induced by these intrinsic motions of MV-H wereinferred by rigidly tethering SCR1 and SCR2 to their interactingresidues in the crystal structure. Diagram mModels of MV-F were producedby Gaussian smoothing of the molecular surface of 1G5G (Chen et al.,Structure, 9:255-66 (2001))—the fusion protein of Newcastle diseasevirus/NDV which, like MV, is a member of the Paramyxoviridae family.

Results

Genome-Wide Analysis Results with Humoral ImmunityGenetic Regions Associated with Variations in Measles-Specific AntibodyResponse after Vaccination

The demographic and immune characteristics of the study sample (n=2,872)are summarized in Table 1. Two independent gene regions on chromosome 1associated with antibody response following measles vaccination wereidentified (FIGS. 1 and 2). As depicted on the locus zoom plot (FIG.1A), the right region on chromosome 1 contained multiple SNPs (n=20)in/around the MV receptor-encoding CD46 gene and region (1q32, bp207917499-208025926, NCBI Build 37/hg19). Analyzing associations betweenantibody response and SNPs in the two other MV receptors on chromosome1, SLAM (SLAMF1) and nectin-4 (NECTIN4/PVRL4), did not result insignificant findings. The left region (FIG. 1C) on chromosome 1 (1p31.1,bp 79082772-79110518) contained nine significant SNPs in/around theinterferon-induced, protein 44-like gene IFI44L.

CD46 Region SNPs Associated with Variations in Measles-Specific AntibodyResponse after Vaccination

The genetic association signal from the 1q32 region was linked to twoblocks (97 kb and 8 kb) of 20 genetic variants in and around the CD46gene (seven intronic CD46 SNPs, four SNPs in the uncharacterizedLOC101929385 (currently Gene ID 100128537, C1orf132 chromosome 1 openreading frame 132), and nine intergenic SNPs, including the previouslyreported rs1318653 (Feenstra et al., Nature Genetics, 46:1274-82(2014)), located between CD46 and CD34), which were in high linkagedisequilibrium (LD) (FIG. 3). The most significant CD46 SNPs, rs2724384and rs2724374 (in high LD, r2=97), lie in intron 1, and near theboundary of intron 8 (of the reference sequence ENST00000358170, RefSeqNM_002389), respectively. The minor alleles (G) of rs2724384 andrs2724374 were significantly associated (Table 2) with an alleledose-related decrease in measles-specific neutralizing antibody titersafter vaccination (46-47% decrease in antibody titer in homozygous minorallele genotype subjects compared to homozygous major allele genotypesubjects, Table 2, FIG. 1B). Due to the high LD (FIG. 3), allsignificant CD46 SNPs displayed similar effects. Most of the 1q32associations remained genome-wide significant (p<5.0×10⁻⁸) in thesubjects of Caucasian ancestry, where the most significant SNP wasrs2724374 (p-value=4.88×10⁻⁹, Table 3).

TABLE 2 Genome-wide significant associations of SNPs withmeasles-specific neutralizing antibody titers after MMR vaccination(combined analysis, n = 2872^(a)). Major Minor Median (IQR) Median (IQR)Median (IQR) SNP ID^(b) Gene/Location^(c) allele allele MAF^(d)P-value^(e) Obs.0^(f) Obs.1^(f) Obs.2^(f) 0^(g) 1^(g) 2^(g) rs1333973IFI44L, intron T A 0.32 1.41E−10 1289 1230 299 1010 (440, 1919)  772(363, 1491)  625 (314, 1304) rs273259 IFI44L, missense A G 0.33 2.87E−101253 1250 315 1003 (438, 1879)  777 (364, 1520)  631 (326, 1304)rs2724384 CD46, intron A G 0.23 2.64E−09 1680  999 139 978 (429, 1882)710 (363, 1468) 516 (272, 884) rs2761437 — G A 0.23 3.14E−09 1671 1003144 981 (431, 1881) 710 (359, 1475) 517 (283, 884) rs2724374 CD46,intron T G 0.23 3.16E−09 1666 1006 146 978 (430, 1881) 717 (361, 1470)526 (277, 884) rs2796265 — T C 0.23 3.70E−09 1671 1002 145 981 (431,1881) 710 (358, 1470) 518 (286, 884) rs4650590 IFI44L, 3 'UTR A G 0.333.72E−09 1266 1226 326 1022 (450, 1932)  755 (361, 1470)  650 (329,1327) rs11118612 LOC101929385 T A 0.23 4.06E−09 1685  991 142 978 (432,1882) 703 (347, 1435) 545 (300, 972) rs2761434 — G A 0.23 4.97E−09 16711002 145 981 (431, 1881) 710 (358, 1463) 518 (286, 884) rs4844392LOC101929385 C G 0.23 5.26E−09 1688  987 143 978 (432, 1882) 707 (345,1443) 545 (301, 952) rs4844619 CD46, intron C T 0.23 5.40E−09 1685  993140 973 (430, 1879) 712 (354, 1462) 539 (291, 891) rs2466572 CD46,intron C A 0.23 6.33E−09 1668 1005 145 978 (430, 1880) 715 (361, 1473)533 (286, 884) rs2724360 CD46, intron T C 0.23 6.51E−09 1664 1009 145980 (430, 1880) 715 (360, 1473) 533 (286, 884) rs6657476 CD46, intron GT 0.23 6.51E−09 1687  991 140 972 (430, 1878) 710 (354, 1462) 539 (291,891) rs56075814 — T C 0.23 9.15E−09 1682  993 143 976 (431, 1879) 708(347, 1450) 545 (301, 952) rs6669384 — T C 0.22 1.06E−08 1711  980 127970 (431, 1884) 709 (349, 1420) 545 (296, 992) rs55935450 — T A 0.221.21E−08 1702  981 135 978 (430, 1885) 703 (348, 1417)  552 (301, 1013)rs6693207 IFI44L, 3' UTR G A 0.33 1.23E−08 1273 1223 322 1023 (455,1932)  753 (354, 1479)  650 (340, 1316) rs273255 IFI44L, intron A T 0.321.24E−08 1311 1222 285 1005 (439, 1873)  771 (362, 1504)  637 (330,1299) rs11118668 — C T 0.22 1.30E−08 1702  981 135 978 (430, 1885) 703(348, 1417)  552 (301, 1013) rs66532523 LOC101929385 A C 0.23 1.45E−081683  992 143 974 (432, 1875) 709 (347, 1455) 545 (301, 952) rs273261IFI44L, intron G A 0.34 2.03E−08 1223 1251 344 997 (438, 1857) 774 (363,1522)  662 (335, 1366) rs4844620 LOC101929385 G A 0.21 2.18E−08 1762 937 119 971 (430, 1876) 701 (347, 1417) 495 (280, 884) rs1318653 — T C0.22 2.94E−08 1708  976 134 972 (430, 1882) 705 (347, 1417)  565 (303,1023) rs273256 IFI44, intron A C 0.36 3.15E−08 1166 1277 375 1002 (445,1898)  774 (362, 1520)  691 (349, 1398) rs273244 IFI44L, intron A T 0.363.30E−08 1162 1280 376 1004 (445, 1898)  772 (362, 1520)  694 (349,1417) rs61821293 — T G 0.22 4.14E−08 1697  984 137 970 (430, 1879) 710(347, 1426) 561 (302, 992) rs273238 — G A 0.35 4.37E−08 1220 1249 349996 (438, 1845) 779 (363, 1528)  658 (338, 1359) rs4844390 CD46, intronA G 0.21 4.63E−08 1753  940 125 974 (427, 1883) 702 (357, 1419) 495(274, 880) ^(a)Reduced to 2818 after excluding subjects with immuneoutcome data that failed QC ^(b)SNP identification number^(c)Gene/genetic region and SNP location relative to the gene ^(d)Minorallele frequency ^(e)P-values ^(f)Number of subjects with homozygousmajor allele genotype (0), heterozygous (1) and homozygous minor allelegenotype (2) ^(g)Median neutralizing antibody titer (in miU/mL, with 25%and 75% inter-quartile range/IQR) for subjects with homozygous majorallele genotype (0), heterozygous (1) and homozygous minor allelegenotype (2)

TABLE 3 Top significant associations of SNPs with measles-specificneutralizing antibody titers after MMR vaccination (Caucasians, n =2555^(a)) Antibody titer Antibody titer Antibody titer Major MinorMedian (IQR) Median (IQR) Median (IQR) SNP ID^(b) Gene/Location^(c)allele allele MAF^(d) P-value^(e) Obs.0^(f) Obs.1^(f) Obs.2^(f) 0^(g)1^(g) 2^(g) rs2724374 CD46, intron T G 0.23 4.88E−09 1462 915 129 924(414, 1799) 703 (352, 1418) 516 (274, 843) rs2761437 G A 0.23 6.98E−091467 912 127 924 (414, 1797) 702 (349, 1422) 515 (280, 825) rs2796265 TC 0.23 8.25E−09 1467 911 128 924 (414, 1797) 702 (349, 1420) 515 (283,847) rs2466572 CD46, intron C A 0.23 9.49E−09 1464 914 128 924 (414,1798) 703 (350, 1418) 517 (283, 847) rs4844619 CD46, intron C T 0.231.05E−08 1468 914 124 916 (414, 1794) 705 (348, 1420) 526 (283, 864)rs6657476 CD46, intron G T 0.23 1.06E−08 1468 914 124 916 (414, 1794)705 (348, 1420) 526 (283, 864) rs2724360 CD46, intron T C 0.23 1.18E−081461 917 128 924 (414, 1798) 703 (349, 1418) 517 (283, 847) rs2761434 GA 0.23 1.19E−08 1467 910 129 924 (414, 1797) 702 (349, 1418) 516 (286,858) rs2724384 CD46, intron A G 0.23 1.27E−08 1466 914 126 924 (414,1798) 702 (354, 1418) 506 (277, 854) rs4844620 LOC101929385 G A 0.231.64E−08 1490 899 117 913 (416, 1772) 701 (345, 1405) 495 (286, 884)rs4844392 LOC101929385 C G 0.23 1.69E−08 1461 917 128 919 (416, 1793)702 (344, 1418) 539 (291, 883) rs11118612 LOC101929385 T A 0.23 1.98E−081461 918 127 918 (416, 1793) 702 (346, 1417) 533 (290, 884) rs1333973IFI44L, intron T A 0.33 2.10E−08 1122 1106 278 942 (422, 1768) 759 (361,1448) 616 (306, 1283) rs66532523 LOC101929385 A C 0.23 2.27E−08 1461 917128 918 (416, 1793) 702 (345, 1417) 539 (291, 883) rs56075814 T C 0.232.34E−08 1460 918 128 917 (416, 1794) 703 (346, 1417) 539 (291, 883)rs273259 IFI44L, missense A G 0.33 2.62E−08 1118 1104 284 942 (424,1765) 757 (356, 1455) 628 (319, 1284) rs273261 IFI44L, intron G A 0.343.41E−08 1110 1106 290 950 (428, 1768) 754 (355, 1441) 631 (323, 1287)rs4844390 CD46, intron A G 0.23 3.48E−08 1478 907 121 919 (414, 1795)702 (352, 1417) 495 (274, 858) rs6669384 T C 0.23 3.75E−08 1484 909 113916 (414, 1797) 703 (349, 1410) 545 (293, 884) rs273256 IFI44L, intron AC 0.35 5.10E−08 1052 1134 320 958 (435, 1806) 743 (347, 1448) 646 (329,1301) rs273244 IFI44L, intron A T 0.35 6.35E−08 1050 1136 320 964 (434,1807) 740 (348, 1438) 646 (329, 1311) rs4650590 IFI44L, 3 'UTR A G 0.356.58E−08 1065 1131 310 945 (432, 1808) 739 (352, 1440) 646 (329, 1316)rs273238 G A 0.34 6.91E−08 1108 1105 293 950 (427, 1766) 758 (355, 1436)630 (327, 1299) rs55935450 T A 0.23 6.93E−08 1477 910 119 916 (414,1793) 700 (347, 1407) 545 (296, 898) rs11118668 C T 0.23 7.38E−08 1477910 119 916 (414, 1793) 700 (347, 1407) 545 (296, 898) rs61821293 T G0.23 8.51E−08 1475 910 121 911 (414, 1790) 702 (345, 1415) 561 (299,884) rs6693207 IFI44L, G A 0.35 9.28E−08 1069 1131 306 956 (434, 1807)740 (346, 1447) 643 (337, 1306) downstream rs273255 IFI44L, intron A T0.32 1.01E−07 1149 1095 262 945 (426, 1769) 735 (348, 1417) 634 (328,1287) rs1318653 T C 0.23 1.04E−07 1480 907 119 909 (414, 1776) 702 (345,1414) 561 (301, 898) ^(a)Reduced to 2506 after excluding subjects withimmune outcome data that failed QC ^(b)SNP identification number^(c)Gene/genetic region and SNP location relative to the gene ^(d)Minorallele frequency ^(e)P-values ^(f)Number of subjects with homozygousmajor allele genotype (0), heterozygous (1) and homozygous minor allelegenotype (2) ^(g)Median neutralizing antibody titer (in miU/mL, with 25%and 75% inter-quartile range/IQR) for subjects with homozygous majorallele genotype (0), heterozygous (1) and homozygous minor allelegenotype (2)IFI44L Region SNPs Associated with Variations in Measles-SpecificAntibody Response after Vaccination

The 1p31.1 region signal was linked to a 21-kb block of 8 IFI44L SNPsand one intergenic SNP, in high LD (FIG. 3). The two most significantIFI44L SNPs, rs1333973 and rs273259 (Table 2) were located in IFI44Lintron 2 (boundary) and IFI44L exon 2, respectively. The missense SNPrs273259 (His73Arg, Ensembl transcript ENST00000370751), as well as theother significant SNPs, demonstrated an allele dose-related decrease inmeasles-specific neutralizing antibody titers (Table 2, FIG. 1D). Threeof the nine SNPs remained genome-wide significant (p<5.0×10⁻⁸) in thesubjects of Caucasian ancestry (Table 3).

To determine if there were multiple SNPs in each of the CD46 and IFI44Lregions associated with the neutralizing antibody, with the effects ofthe SNPs adjusted for each other, elastic net was used to select SNPs.An advantage of elastic net is that it can select highly correlatedSNPs, although it cannot give p-values for selected SNPs. Hence, afterselection, the selected SNPs were evaluated in linear regression models.This resulted in the selection of two SNPs in the CD46 region and threeSNPs in the IFI44L region, based on the Caucasian subjects. For the CD46region, rs2724374 was found to be the most significant and the primarydriving SNP (p=4.3×10⁻⁸), with rs11806810 having much less association(p=0.02) when the effects of the SNPs were adjusted for each other. Forthe IFI44L region, the SNPs rs12026737, rs1333973, and rs273259 wereselected. However, rs273259 and rs1333973 were highly correlated(r²=0.99), making it difficult to disentangle their effects and fit bothin a regression model. When choosing rs1333973 (top significant SNP)over rs273259, rs1333973 (p=2×10⁻⁸) and rs12026737 (p=6.0×10⁻⁴) werefound to have strong statistical associations, with effects adjusted foreach other. Furthermore, the CD46 and IFI44L regions have associationsthat are independent of each other (since when the aforementioned SNPswere modeled together, the results were not significantly different fromwhat was obtained when the regions were modeled separately).

Genome-Wide Analysis Results with Measles Vaccine Cellular Immunity

The GWAS analyses did not reveal significant SNP associations withcellular immunity after vaccination, as measured by MV-specific IFNγELISPOT (Table 4, FIG. 4). Analyses of all chromosome 1 SNPs withMV-specific secreted cytokines in 625 Caucasian subjects (for whomcytokine data was available) demonstrated suggestive associationsbetween CD46 SNPs (including rs2724374 and rs2724384) and the secretionof IFNγ; however, an allele-dose-dependency of IFNγ secretion was notnoted (Table 5).

TABLE 4 Top 20 genome-wide associations of SNPs with measles-specificIFNγ ELISPOT response after MMR vaccination (Combined analysis, n =2872^(a)) IFNg IFNg IFNg ELISOT ELISOT ELISOT Major Minor Median MedianMedian SNP ID^(b) Chr. Gene^(c) allele allele MAF^(d) P-value^(e)Obs.0^(f) Obs1^(f) Obs.2^(f) (IQR) 0^(g) (IQR) 1^(g) (IQR) 2^(g)rs140973961 6 HLA-DRB5 G C 0.34 1.05E−06 1138 1202 278 13 (6, 31) 15 (6,33) 19 (8, 40) rs115793823 6 — T C 0.24 1.25E−06 1479 1022 117 16 (7,36) 14 (6, 30) 12 (5, 25) rs115742047 6 — A G 0.26 2.18E−06 1422 1023173 16 (7, 36) 14 (6, 30) 11 (5, 25) rs116117104 6 — T C 0.26 2.62E−061412 1035 171 16 (7, 36) 14 (6, 30) 11 (5, 24) rs114317125 6 — C T 0.262.63E−06 1412 1035 171 16 (7, 36) 14 (6, 30) 11 (5, 24) rs116663036 6 —G A 0.26 2.63E−06 1412 1036 170 16 (7, 36) 14 (6, 30) 11 (5, 25)rs182191708 6 HLA-DRB5 A C 0.30 2.94E−06 1253 1154 211 16 (7, 35) 14 (6,32) 12 (5, 31) rs114027708 6 — A G 0.23 2.98E−06 1546  939 133 16 (7,35) 13 (5, 30) 13 (6, 26) rs114854965 6 — C T 0.27 3.00E−06 1395 1051172 16 (7, 37) 14 (6, 30) 11 (5, 24) rs116230731 6 — C T 0.26 3.22E−061404 1041 173 16 (7, 36) 14 (6, 30) 11 (5, 24) rs115383757 6 — T A 0.263.22E−06 1404 1041 173 16 (7, 36) 14 (6, 30) 11 (5, 24) rs114274063 6 —T G 0.27 3.25E−06 1400 1047 171 16 (7, 37) 14 (6, 30) 11 (5, 24)rs115052056 6 — T A 0.27 3.25E−06 1400 1047 171 16 (7, 37) 14 (6, 30) 11(5, 24) rs115613143 6 — C T 0.26 3.26E−06 1435 1021 162 16 (7, 36) 14(6, 30) 12 (5, 26) rs114634027 6 — A G 0.27 3.30E−06 1400 1047 171 16(7, 37) 14 (6, 30) 11 (5, 24) rs114250489 6 — G A 0.25 3.43E−06 14481045 125 16 (7, 36) 14 (6, 30) 12 (5, 25) rs114759127 6 — T A 0.263.43E−06 1430 1025 163 16 (7, 36) 14 (6, 30) 11 (5, 24) rs115751649 6 —T C 0.26 3.44E−06 1405 1040 173 16 (7, 36) 14 (6, 30) 11 (5, 25)rs114332144 6 — C T 0.27 3.45E−06 1401 1045 172 16 (7, 37) 14 (6, 30) 11(5, 25) rs115712303 6 — C G 0.27 3.45E−06 1391 1053 174 16 (7, 37) 14(6, 30) 11 (5, 25) ^(a)Reduced to 2618 after excluding subjects withimmune outcome data that failed QC ^(b)SNP identification number^(e)Gene/genetic region ^(d)Minor allele frequency ^(e)P-values^(f)Number of subjects with homozygous major allele genotype (0),heterozygous (1), and homozygous minor allele genotype (2) ^(g)Medianmeasles virus-specific ELISPOT response (IFNγ-positive spot-formingunits/SFUs per 2 × 10⁵ cells, with 25% and 75% inter-quartile range/IQR)for subjects with homozygous major allele genotype (0), heterozygous (1)and homozygous minor allele genotype (2)

TABLE 5 Associations between chromosome 1 SNPs and measlesvirus-specific secreted IFNα (Caucasians, n = 625 subjects withavailable measles virus-specific cytokine data) Major Minor Median inMedian in Median in SNP ID^(a) Gene/Location^(b) allele allele MAF^(c)P-value^(d) Obs.0^(e) Obs.1^(e) Obs.2^(e) pg/mL, IQR 0^(f) pg/mL, IQR1^(f) pg/mL, IQR 2^(f) rs2724374 CD46, intron T G 0.23 0.0003 365 232 27508 (251,915) 657 (329,1169) 575 (299,1181) rs2761437 — G A 0.23 0.0001367 230 27 508 (247,914) 656 (327,1178) 749 (370,1181) rs2796265 — T C0.23 0.0002 367 229 28 508 (247,914) 660 (330,1183) 662 (319,1140)rs2466572 CD46, intron C A 0.23 0.0003 366 231 27 510 (251,914) 660(328,1174) 575 (299,1181) rs4844619 CD46, intron C T 0.23 0.0005 368 22927 510 (252,919) 660 (326,1164) 575 (299,1181) rs6657476 CD46, intron GT 0.23 0.0005 368 229 27 510 (252,919) 660 (326,1164) 575 (299,1181)rs2724360 CD46, intron T C 0.23 0.0003 366 231 27 510 (251,914) 660(328,1174) 575 (299,1181) rs2761434 — G A 0.23 0.0002 367 229 28 508(247,914) 660 (330,1183) 662 (319,1140) rs2724384 CD46, intron A G 0.230.0003 367 230 27 508 (252,914) 661 (327,1178) 575 (299,1181) rs4844620LOC101929385 G A 0.22 0.0004 374 228 22 515 (253,926) 656 (322,1185) 662(296,1221) rs4844392 LOC101929385 C G 0.23 0.0003 369 227 28 508(243,915) 660 (328,1152) 662 (319,1278) rs11118612 LOC101929385 T A 0.230.0003 367 229 28 511 (252,922) 652 (323,1139) 662 (319,1278) rs1333973IFI44L, intron T A 0.33 0.4369 286 267 71 579 (256,1013) 568 (281,1020)550 (320,1110) rs66532523 LOC101929385 A C 0.23 0.0003 369 227 28 508(243,915) 660 (328,1152) 662 (319,1278) rs56075814 — T C 0.23 0.0003 367229 28 511 (252,922) 652 (323,1139) 662 (319,1278) rs273259 IFI44L,missense A G 0.33 0.4446 285 266 73 580 (255,1019) 558 (280,1013) 576(324,1099) rs273261 IFI44L, intron G A 0.33 0.4955 285 264 75 580(255,1019) 558 (279,1018) 576 (335,1072) rs4844390 CD46, intron A G 0.220.0002 369 230 25 511 (252,913) 661 (327,1187) 575 (260,1100) rs6669384— T C 0.22 0.0016 371 234 19 523 (256,957) 645 (320,1138) 575 (331,1181)rs273256 IFI44L, intron A C 0.35 0.3759 269 268 87 578 (236,996) 558(280,1042) 576 (335,1041) rs273244 IFI44L, intron A T 0.35 0.4476 267271 86 580 (255,996) 550 (278,1042) 575 (329,1023) rs4650590 IFI44L, 3'UTR A G 0.35 0.2434 274 266 84 572 (241,989) 569 (287,1042) 575(315,1104) rs273238 — G A 0.33 0.5265 284 266 74 582 (257,1025) 558(278,1021) 563 (329,1043) rs55935450 — T A 0.22 0.0007 373 227 24 518(251,952) 652 (325,1152) 662 (251,1140) rs11118668 — C T 0.22 0.0007 373227 24 518 (251,952) 652 (325,1152) 662 (251,1140) rs61821293 — T G 0.220.0005 372 228 24 512 (249,936) 656 (329,1169) 662 (251,1140) rs6693207IFI44L, G A 0.35 0.2152 276 263 85 572 (255,986) 569 (280,1042) 576(324,1099) downstream rs273255 IFI44L, intron A T 0.31 0.4163 300 258 66574 (254,996) 569 (287,1038) 563 (318,1100) rs1318653 T C 0.22 0.0012373 227 24 512 (251,952) 652 (328,1152) 662 (251,1140) ^(a)SNPidentification number ^(b)Gene/genetic region and SNP location relativeto the gene ^(e)Minor allele frequency ^(d)P-values ^(e)Number ofsubjects with homozygous major allele genotype (0), heterozygous (1),and homozygous minor allele genotype (2) ^(f)Median cytokine level (inpg/mL, with 25% and 75% inter-quartile range/IQR) for subjects withhomozygous major allele genotype (0), heterozygous (1) and homozygousminor allele genotype (2)Analysis of Differential Usage of Exons Using mRNA-Seq Data

In the CD46 analyses, a highly significant per-exon estimate(q=2.96×10⁻⁷) with lower exon B (in the CD46 STP region) expression(exon skipping) was observed in subjects with rs2724374 minor G allele(FIG. 5A). These results were further confirmed by RT-PCR analysis ofcommon CD46 isoforms in PBMCs. In this analysis, the predominant “lowerband” CD46 isoform phenotype (C2, associated with exon B skipping) wasclearly more pronounced in the homozygous minor G allele genotypesubjects (FIG. 5B). Differential exon usage based on IFI44Lrs1333973/rs273259 genotypes also was observed (FIG. 5C).

Simulation of the Structural Differences Between CD46 Isoforms (with orwithout the STP Exon B)

Structural models of the predominant CD46 isoforms (extracellularportion) were generated: isoforms with the STP exons B and C (i.e., BC1and BC2) and those skipping exon B (i.e., C1 and C2) (FIGS. 6, 7, and8). The longest isoform, ABC1, generates a high-quality homology model(FIG. 8). Interestingly, the protein sequences encoded by exons A (exon7) and B (exon 8) have their N- and C-terminal ends close to each other.The amino acids encoded by exon A (exon 7) make a short beta strandwithin the STP domain. Deletion of these residues by exon skippingremoves this strand from the beta-sheet, but the architecture of thedomain is not significantly altered. Exon B (8) encodes amino acidsmaking up two additional strands. In the isoforms C1 and C2, only twostrands encoded by exons 9 and 10 remain. Computing the dynamics of eachisoform's atomic model, the smaller STP domain isoforms exhibitedgreater flexibility and less collective motion (i.e., in the C1/C2isoforms when compared to BC1/BC2 of the common isoforms). Monitoringthe domain-domain angles about the SCR4-STP hinge as each structure isdeformed about its low-frequency normal modes, the shorterisoform/isoforms exhibited a greater range of flexibility (FIG. 8). Asillustrated in FIG. 7, based on data from the molecular models, thedifferential isoform flexibility may influence the rate of formation ofthe CD46-MV-hemagglutinin (H) encounter complex, and/or influence thepropensity for MV-H to undergo the conformational change necessary totrigger MV fusion protein.

Other Embodiments

It is to be understood that while the invention has been described inconjunction with the detailed description thereof, the foregoingdescription is intended to illustrate and not limit the scope of theinvention, which is defined by the scope of the appended claims. Otheraspects, advantages, and modifications are within the scope of thefollowing claims.

What is claimed is:
 1. A method for treating a human having cancer,wherein said method comprises: (a) detecting the presence of the majorallele T of CD46 rs2724374, the major allele A of CD46 rs2724384, themajor allele A of IFI44L rs273259, the major allele T of IFI44Lrs1333973, the major allele C of CD46 rs4844619, the major allele C ofCD46 rs2466572, the major allele T of CD46 rs2724360, the major allele Gof CD46 rs6657476, the major allele A of CD46 rs4844390, the majorallele A of IFI44L rs4650590, the major allele G of IFI44L rs6693207,the major allele A of IFI44L rs273255, the major allele G of IFI44Lrs273261, the major allele A of IFI44L rs273256, the major allele A ofIFI44L rs273244, the major allele T of LOC101929385 rs11118612, themajor allele C of LOC101929385 rs4844392, the major allele A ofLOC101929385 rs66532523, the major allele G of LOC101929385 rs4844620,the major allele G of intergenic rs2761437, the major allele T ofintergenic rs2796265, the major allele G of intergenic rs2761434, themajor allele T of intergenic rs56075814, the major allele T ofintergenic rs6669384, the major allele T of intergenic rs55935450, themajor allele C of intergenic rs11118668, the major allele T ofintergenic rs1318653, the major allele T of intergenic rs61821293, themajor allele G of intergenic rs273238, the major allele A of intergenicrs12026737, or the minor allele C of CD46 rs11806810 in a sampleobtained from said human, and (b) administering a measles virus-basedoncolytic treatment to said human.
 2. The method of claim 1, whereinsaid method comprise detecting the presence of the major allele T ofCD46 rs2724374, the major allele A of CD46 rs2724384, the major allele Aof IFI44L rs273259, the major allele T of IFI44L rs1333973, the majorallele C of CD46 rs4844619, the major allele C of CD46 rs2466572, themajor allele T of CD46 rs2724360, the major allele G of CD46 rs6657476,the major allele A of CD46 rs4844390, the major allele A of IFI44Lrs4650590, the major allele G of IFI44L rs6693207, the major allele A ofIFI44L rs273255, the major allele G of IFI44L rs273261, the major alleleA of IFI44L rs273256, the major allele A of IFI44L rs273244, the majorallele T of LOC101929385 rs11118612, the major allele C of LOC101929385rs4844392, the major allele A of LOC101929385 rs66532523, the majorallele G of LOC101929385 rs4844620, the major allele G of intergenicrs2761437, the major allele T of intergenic rs2796265, the major alleleG of intergenic rs2761434, the major allele T of intergenic rs56075814,the major allele T of intergenic rs6669384, the major allele T ofintergenic rs55935450, the major allele C of intergenic rs11118668, themajor allele T of intergenic rs1318653, the major allele T of intergenicrs61821293, the major allele G of intergenic rs273238, the major alleleA of intergenic rs12026737, and the minor allele C of CD46 rs11806810 insaid sample.
 3. A method for treating a human having cancer, whereinsaid method comprises: (a) detecting the presence of the minor allele Gof CD46 rs2724374, the minor allele G of CD46 rs2724384, the minorallele G of IFI44L rs273259, the minor allele A of IFI44L rs1333973, theminor allele T of CD46 rs4844619, the minor allele A of CD46 rs2466572,the minor allele C of CD46 rs2724360, the minor allele T of CD46rs6657476, the minor allele G of CD46 rs4844390, the minor allele G ofIFI44L rs4650590, the minor allele A of IFI44L rs6693207, the minorallele T of IFI44L rs273255, the minor allele A of IFI44L rs273261, theminor allele C of IFI44L rs273256, the minor allele T of IFI44Lrs273244, the minor allele A of LOC101929385 rs11118612, the minorallele G of LOC101929385 rs4844392, the minor allele C of LOC101929385rs66532523, the minor allele A of LOC101929385 rs4844620, the minorallele A of intergenic rs2761437, the minor allele C of intergenicrs2796265, the minor allele A of intergenic rs2761434, the minor alleleC of intergenic rs56075814, the minor allele C of intergenic rs6669384,the minor allele A of intergenic rs55935450, the minor allele T ofintergenic rs11118668, the minor allele C of intergenic rs1318653, theminor allele G of intergenic rs61821293, the minor allele A ofintergenic rs273238, the minor allele C of intergenic rs12026737, or themajor allele G of CD46 rs11806810 in a sample obtained from said human,and (b) administering a modified measles virus-based oncolytic treatmentor a non-measles virus-based oncolytic treatment to said human.
 4. Themethod of claim 3, wherein said method comprise detecting the presenceof the minor allele G of CD46 rs2724374, the minor allele G of CD46rs2724384, the minor allele G of IFI44L rs273259, the minor allele A ofIFI44L rs1333973, the minor allele T of CD46 rs4844619, the minor alleleA of CD46 rs2466572, the minor allele C of CD46 rs2724360, the minorallele T of CD46 rs6657476, the minor allele G of CD46 rs4844390, theminor allele G of IFI44L rs4650590, the minor allele A of IFI44Lrs6693207, the minor allele T of IFI44L rs273255, the minor allele A ofIFI44L rs273261, the minor allele C of IFI44L rs273256, the minor alleleT of IFI44L rs273244, the minor allele A of LOC101929385 rs11118612, theminor allele G of LOC101929385 rs4844392, the minor allele C ofLOC101929385 rs66532523, the minor allele A of LOC101929385 rs4844620,the minor allele A of intergenic rs2761437, the minor allele C ofintergenic rs2796265, the minor allele A of intergenic rs2761434, theminor allele C of intergenic rs56075814, the minor allele C ofintergenic rs6669384, the minor allele A of intergenic rs55935450, theminor allele T of intergenic rs11118668, the minor allele C ofintergenic rs1318653, the minor allele G of intergenic rs61821293, theminor allele A of intergenic rs273238, the minor allele C of intergenicrs12026737, and the major allele G of CD46 rs11806810 in said sample.